Check out the individual Season 5 review here.

Season 5, Episode 1 – Aired: 7/11/2008 – Search and Rescue (2)

Colonel Carter attempts to lead a rescue mission to save several trapped Atlantis team members, unaware that Michael is closing in on their position with a heavy cruiser.

Much of this episode takes place in the rubble of Michael’s destroyed complex, where many of the Atlantis personnel are trapped in the ruins, including Sheppard, Ronon and McKay.  But the action eventually leads aboard Michael’s ship where the team has to rescue Teyla and her newborn son.  Hewlett shines as an exasperated  McKay who has to deliver Teyla’s baby.  It’s a solid episode, but probably the least of the season premieres.

Season 5, Episode 2 – Aired: 7/18/2008 – The Seed

After Dr. Keller removes Beckett from stasis, she gets infected with a dangerous entity that begins taking over Atlantis.

This is simply a bizarre episode where Keller gets infected by a Wraith hive ship of all things.  Just weird.

Season 5, Episode 3 – Aired: 7/25/2008 – Broken Ties

Ronon is captured by his former friend Tyre, who plans to turn him over to the Wraith to get back in their good graces.

Good wrap up to the previous season’s storyline between Ronon and Tyre, as Ronon is betrayed by his friend and delivered to the Wraith, where Ronon is converted into a Wraith worshipper, and Tyre has tom detox from the enzyme in order to save his friend.  You thought heroin detox was bad, you haven’t tripped on Wraith enzyme and then had to come off of it.  Wow.

Season 5, Episode 4 – Aired: 8/1/2008 – The Daedalus Variations

Sheppard’s team finds the Earth ship Daedalus abandoned and without power.

This is a multiple realities episode where the team gets trapped on an alternate Daedalus that has been skipping dimensions.  A new race of bad guys is introduced this episode, and I firmly believe, that if the show had continued for more seasons, they would have probably been the new bad guys as the Wraith had essentially been played out by then.

Season 5, Episode 5 – Aired: 8/15/2008 – Ghost in the Machine

When Sheppard and his team are about to return from an off world mission with their Puddle Jumper, the systems of the Jumper go crazy. Barely able to return to Atlantis, the Jumper seems to infect the city’s systems with what seems to be a computer virus.

Season 5, Episode 6 – Aired: 8/22/2008 – The Shrine

McKay begins to lose his memory after contracting the Pegasus version of Alzheimer’s called “Second Childhood.”

I’ve gone on about this episode in my previous review of Season 5.  It’s one of the best of the entire series and features stellar work by Hewlett as McKay.  Easily his best episode of the entire series run.  Just a really heartfelt installment.  Really enjoyed it.  Key scene: Sheppard and McKay sharing beers on the Atlantis docks, knowing that Rodney is slipping away and he can’t be saved.

Season 5, Episode 7 – Aired: 9/5/2008 – Whispers

Sheppard and Beckett are terrorized by deadly creatures on a planet housing one of Michael’s research facilities.

If there was an episode that was like The Descent, this is it, as the team finds themselves on a planet with remnants from one of Michael’s experiments.  The creatures hunt by sound and are blind.

Season 5, Episode 8 – Aired: 9/12/2008 – The Queen

Sheppard’s team accompanies Todd the Wraith on a mission to negotiate an alliance with another Hive with Teyla playing a key role when she’s surgically altered to be a Wraith Queen.

Season 5, Episode 9 – Aired: 9/19/2008 – Tracker

Keller is abducted on a trip off world to help a wraith-threatened village, and it’s up to Ronon and McKay to find her. However it soon emerges that her abductor is, in fact, a Runner.

Season 5, Episode 10 – Aired: 9/26/2008 – First Contact (1)

Daniel Jackson visits Atlantis to do some research on the Ancient scientist Janus.

Season 5, Episode 11 – Aired: 10/10/2008 – The Lost Tribe (2)

Sheppard must rescue McKay and Daniel Jackson from an Ancient laboratory that belonged to Janus before Todd, who has hijacked the Daedalus, gets there first.

These two episodes were a welcome return for Daniel Jackson to the series, and a major surprise for who the villains were.  The plot basically involves the villains’ use of a device that negates Wraith hyperdrive technology, but has an explosive side effect regarding the Stargates.  Good effect of a Stargate going boom in the Atlantis control tower and a space battle in the second episode.  McKay and Daniel also have good interplay.

Season 5, Episode 12 – Aired: 10/17/2008 – Outsiders

When the Wraith discover that a small group of survivors of Michael’s release of the modified Hoffan drug are hiding among the population of a village on another planet, Sheppard and his team must convince the entire village to evacuate before a Hive Ship arrives.

Season 5, Episode 13 – Aired: 10/24/2008 – Inquisition

When Sheppard and his team are brought to trial by a Coalition of human worlds for what they claim are crimes against the people of the galaxy, it’s up to Woolsey’s legal expertise to clear their names.

Season 5, Episode 14 – Aired: 11/7/2008 – The Prodigal

Michael besieges Atlantis in an attempt to kidnap Teyla’s infant child.

Satisfying conclusion to Michael’s story arc, and a good Teyla-centric episode.

Season 5, Episode 15 – Aired: 11/14/2008 – Remnants

While exploring the mainland of Atlantis’ planet, Sheppard is captured by a foe believed to be long dead. Meanwhile, Woolsey’s job is at risk and he has an important decision to make and McKay and Zelenka make an interesting undersea discovery.

This was a rare clunker episode and featured masquerading aliens as an old foe.

Season 5, Episode 16 – Aired: 11/21/2008 – Brain Storm

McKay returns to Earth to witness the unveiling of his rival’s latest breakthrough.

Season 5, Episode 17 – Aired: 12/5/2008 – Infection

When a Wraith Hive Ship arrives in orbit above Atlantis and sends a distress message, Sheppard takes a team to investigate and discovers that the Wraith have been infected with a strange disease.

Season 5, Episode 18 – Aired: 12/12/2008 – Identity

A thief uses an Ancient transfer device to switch her consciousness with Dr. Keller. While she attempts to escape Atlantis, Dr. Keller must deal with the thief’s accomplices and angry villagers on her trail.

Season 5, Episode 19 – Aired: 1/2/2009 – Vegas

Detective John Sheppard investigates a series of unusual murders in Las Vegas.

Quite a departure for the series.  This took place in the alternate reality that the alternate McKay was from in the “McKay and Mrs. Miller” episode.  Actual location shooting in Vegas and a pretty good story, showing a burned out Sheppard as a cop tracking down a Wraith who’s on a bender in Vegas.  Before he’s caught, the Wraith sends out a signal that has consequences for Atlantis in our reality.

Season 5, Episode 20 – Aired: 1/9/2009 – Enemy at the Gate

Todd informs Atlantis that a rogue Wraith has acquired several ZPMs to power a formidable new Hive ship. When the Daedalus engages it in battle but is unable to defeat it, the team gets a message indicating it is headed to Earth.

I rewatched this and enjoyed it just a bit more than before, although the shortfalls of things that we would have liked to see, like the Super Hive engaging the Apollo and Sun-Tzu in battle, plus the fabled wormhole drive that Atlantis uses to instantly get to Earth.  Obviously those things were sacrificed due to budget or time or both, because Atlantis wasn’t in the habit of skimming on the effects.  This was a satisfying ending to the show, which should have had at least one more season.  If I didn’t like Stargate: Universe, I’d be a bit more perturbed that Atlantis was gone.  I thought that the show got past the cast shakeups with Higginson, Tapping and finally Picardo.  Having Atlantis back on Earth could have opened up an entire new avenue for storytelling.  I hope they follow through on plans for an Atlantis movie.
There are three major arcs working in Season 4.  The first is the ultimate fate of Dr. Weir, the second the Replicator / Wraith War and the collateral damage it ends up causing, and what happened to Teyla’s people, the Athosians, including the father of her baby, Kanan.  This is also the season where Amanda Tapping joins the cast, replacing Torri Higginson…and not necessarily to the betterment of the show. 

Season 4, Episode 1 – Aired: 9/28/2007 – Adrift (2)

With only 24 hours of power left, and unable to use the Stargate, the Atlantis team must once again save the city from certain doom, while Dr. Weir struggles to survive.

Season 4, Episode 2 – Aired: 10/5/2007 – Lifeline (3)

While Carter and the Apollo search for missing city of Atlantis, Sheppard and his team risk their lives on a mission to steal a ZPM from the Replicators.

Adrift may have been the best season premiere of the entire series run, because it features multiple problems for Atlantis on multiple fronts, all concerning the city’s diminishing power and failing shield in the depths of space.  Also, Weir was fighting for her life in a seemingly losing battle.  This featured a lot of cool space action, including having to use jumpers to blast a path though an asteroid field for the city.  Sheppard and Zelenka also have a nifty space walk to perform.  Rodney of course has to come up with a solution that involves a daring raid on the Replicators.  it also features tension between Sheppard and McKay when McKay activates the dormant Replicator nanites in Weir’s body to fix her brain injury, against Sheppard’s orders.  “Lifeline” featured not only Sheppard’s team’s raid on Replicator City, but Carter looking for a way to contact Atlantis.  The resolution of this three part story arc led to Weir going missing and thus Torri Higginson’s departure from the show, again, to my dismay.  Amanda Tapping then joined the cast as the new leader of Atlantis until Weir could be found.

Season 4, Episode 3 – Aired: 10/12/2007 – Reunion

Ronon is reunited with a group of his fellow Satedans who ask him to leave Atlantis and join them. Colonel Samantha Carter arrives at Atlantis to assume command.

Good action episode that featured Mark Dacascos as a fellow Satedan to Ronon who ends up betraying him when it’s discovered he’s been turned by a process the Wraith use involving repeatedly feeding on humans and then restoring them in order to get them hooked on the Wraith enzyme.  Some good Satedan-on-Satedan battle action in the climax.

Season 4, Episode 4 – Aired: 10/19/2007 – Doppelganger

After discovering a crystal entity, the team begins to have nightmares involving Sheppard.

Season 4, Episode 5 – Aired: 10/26/2007 – Travelers

Sheppard is captured by a space-faring race who wish to use his Ancient gene for their own ends.

Good Sheppard-centric episode that finds him matching wits with a hot commander (Jill Wagner) of a space faring people who find an Ancient battleship that they need Sheppard to fly.  Sheppard has to play cat and mouse with not only his captors, but some Wraith as well.  I was kind of disappointed though, that they hinted at the origin of Ronon’s famed space revolver gun, but not how he came to get it.  Jill Wagner in leather is always welcome, though.

Season 4, Episode 6 – Aired: 11/2/2007 – Tabula Rasa

When a deadly infection causes key members of Atlantis to lose their memories, it’s up to Teyla and Ronon to find a cure. But when the Marines begin hunting down everyone and no one remembers why, it’s hard to work together to cure everyone.

Another tried (tired) and true genre show staple: everybody loses their memories and have to rediscover who they are.  A similar episode occurred on not only Buffy (Tabula Rasa) and Angel (Spin The Bottle), but even SG-1 itself (Beneath the Surface).

Season 4, Episode 7 – Aired: 11/9/2007 – Missing

During a visit to New Athos, Teyla and Dr. Keller find themselves on the run from a primitive tribe of warriors and Teyla makes a shocking discovery.

Season 4, Episode 8 – Aired: 11/16/2007 – The Seer

The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis’ future. Meanwhile, they join forces with a Wraith in an attempt to fix the virus Rodney created earlier to stop the Replicators, that has since malfunctioned. Woolsey arrives at Atlantis to conduct an evaluation of Carter’s command.

Season 4, Episode 9 – Aired: 11/30/2007 – Miller’s Crossing

After McKay and his sister Jeanie Miller are kidnapped on Earth, Sheppard and Ronon must enlist the help of the NID to find them.

Season 4, Episode 10 – Aired: 12/7/2007 – This Mortal Coil (1)

When a mysterious probe crashes into the city the team is convinced the Replicators have found them.

Season 4, Episode 11 – Aired: 1/4/2008 – Be All My Sins Remember’d (2)

With a way to finally track the Replicators ships, the Atlantis team must come up with a way to finally be rid of the Replicators once and for all.

Season 4, Episode 12 – Aired: 1/11/2008 – Spoils of War (3)

The team obtains a Wraith Hive ship after the battle with the Replicators and learn something new about their enemy.

This Mortal Coil, Be All My Sins Remember’d, and Spoils of War are another mini-arc within the season that deals with the final confrontation with the Replicators.  Coil deals with Replicator duplicates of Sheppard’s team becoming self aware after thinking they’re the real deal.  It’s also presented in this episode that Weir was indeed killed by the Replicators, even though the duplicate has all of her memories.  Be All My Sins Remember’d features the biggest team up of ships to unite against the Replicators in a daring plan by Rodney to use a human form Replicator named FRAN to destroy them once and for all.  Some good space battles and an impressive finale that features a massive clumping of Replicators on their planet, leading to their destruction, and a surprise return of a character (Weir), as a Replicator?  Spoils of War is a sort of epilogue to that battle, dealing with Teyla and her pregnancy on a mission to destroy a Wraith cloning facility.  Coil was a disappointing episode, because almost the same concept had been done on SG-1, with androids who thought they were the real SG-1 team (Tin Man).  It’s part of the final arc for Weir which I didn’t like.  It’s also the final appearance for Torri Higginson on the show.

Season 4, Episode 13 – Aired: 1/18/2008 – Quarantine

When Atlantis is put under quarantine, everyone gets stuck in a room with another person. While dealing with personal issues, they also try to figure out why there’s a quarantine, and how to get out.

Season 4, Episode 14 – Aired: 1/25/2008 – Harmony

While accompanying a princess on a pilgrimage to become queen Sheppard and McKay encounter a familiar foe.

Season 4, Episode 15 – Aired: 2/1/2008 – Outcast

After the death of his father, Sheppard returns to Earth where he learns that scientists have created a human-form Replicator that is now on the loose.

Season 4, Episode 16 – Aired: 2/8/2008 – Trio

Colonel Carter joins Dr. McKay and Dr. Keller on an off-world mission, to convince the people of a world rocked by earthquakes, to relocate. However, things take a turn for the worst when they are plunged into a sinkhole and become trapped in an old Genii mining facility.

This is a “they fell into a hole” episode that wasn’t very interesting.  Carter falls from a great height not once, not twice, but three times.  Fairly boring installment.

Season 4, Episode 17 – Aired: 2/15/2008 – Midway

When Colonel Carter invites Teal’C to Atlantis to counsel Ronon, who is up for review by the I.O.A., word comes in that the Wraith have discovered the now fully operational Midway Space Station.

Midway is one of the best episodes of the season.  It features a confrontation that Stargate fans had been hoping for for years: Teal’C vs. Ronon.  And it didn’t disappoint.  The two have a sparring session that lasts over an hour without producing a winner.  And later, Teal’C and Ronon get stuck on the Midway station between Atlantis and Earth and have to deal with a contingent of Wraith invaders who are looking to use the Stargate system to get to Earth.  Plenty of good Wraith dispatching to be found in this episode.  Also a nice nod to the fans to have Ronon ask Teal’C why he says “indeed” all the time and Teal’C be oblivious that that was an annoying habit of his.

Season 4, Episode 18 – Aired: 2/22/2008 – The Kindred (1)

While a disease spreads through the Pegasus Galaxy, Teyla believes the father of her child is trying to communicate with her. While searching for answers, the team comes across a very interesting discovery.

Season 4, Episode 19 – Aired: 2/29/2008 –
The Kindred (2)After finding some of the missing Athosians, Teyla plans an escape from Michael’s secret facility. Meanwhile, Keller investigates the origins of the Beckett duplicate.

Season 4, Episode 20 – Aired: 3/7/2008 – The Last Man (1)

Sheppard returns from a mission and finds Atlantis abandoned and surrounded by sand dunes. He soon finds a hologram of Dr. McKay, who tells him he has come 48,000 years into the future, and everyone is long dead. But the McKay hologram has a plan to save the city and restore Sheppard to his own time.

The Last Man is a good season finale that makes use of the wormhole time travel / solar flare effect introduced in the SG-1 episode, 1969, and also in the Stargate: Continuum movie.  Except this time, Sheppard is the one who time travels, and it’s some 48,000 years into the future, where Atlantis is an abandoned facility in the middle of a desert.  He’d be screwed if McKay hadn’t figured out a way to save a little of himself for the future to help Sheppard out.  So the whole exercise ends up being an alternate future kind of deal, where, as they’re working on McKay’s plan to get Sheppard back to the future, he recounts how things went to shit for the entire Atlantis expedition after Sheppard disappeared.  Basically everyone died except McKay, who spent the rest of his life trying to figure out a way to change things, including finding Teyla, who was due to give birth soon before Sheppard disappeared.  Good interaction between McKay and Sheppard, as they basically carry the entire episode.  Also ends on an explosive note, literally.

Season 3, Episode 1 – Aired: 7/14/2006 – No Man’s Land (2)

Two Wraith Hive ships have captured Dr. McKay and Ronon and are on their way to Earth. It is up to Colonel Sheppard to rescue them and figure out a way to stop the Wraith from reaching a “new feeding ground”.

Season 3, Episode 2 – Aired: 7/21/2006 – Misbegotten (3)

After turning a Wraith hive ship crew into humans, the Atlantis team must decide on their fate. Meanwhile, Dr. Weir finds herself under the scrutiny of Richard Woolsey and the I.O.A.

No Man’s Land and Misbegotten continues the two-parter that begun with the Season 2 finale.  Once again, members of Sheppard’s team find themselves prisoners on a Wraith ship.  But this one is heading to Earth.  The only person that can help them is one of their most dangerous enemies: Michael.  Apparently, he’s stuck in limbo, no longer a human but not accepted by the Wraith.  Which spins his arc into a new direction later on down the line.  Lot of good space action in No Man’s Land and another dilemma when the retrovirus is unleashed upon the Wraith, leaving a ship full of devolved Wraith/human prisoners with no memory of who they really are, including Michael…again.

Season 3, Episode 3 – Aired: 7/28/2006 – Irresistible

A man from another world has an unusual effect on the Atlantis team, causing them to behave strangely. The few unaffected team members must uncover the cause.

Season 3, Episode 4 – Aired: 8/4/2006 – Sateda

Sheppard, Teyla and Ronon come under attack on a forested world. Ronon, realizing that he has been on the planet before, learns that his earlier visit came with harsh consequences.

This is one of the best episodes not only of the season, but the entire series.  If you like Ronon flaying Wraithflesh, this is the episode to catch.  Ronon finds an unwanted consequence from his days as a runner, the destruction of a village in which he took refuge for a night years earlier, breaking his rule to not associate with anyone for fear of bringing the Wraith to them.  When he’s captured by the Wraith who initially turned him into a runner, Ronon is deposited back on Sateda for the Wraith’s sport.  He has to come to terms with the destruction of his world and the life he was forced to leave behind.  He dispatches Wraith upon Wraith in order to lure the leader down for a final confrontation.  Even though Sheppard and the others show up to rescue him, Ronon won’t go until the Wraith who’s responsible for his misery is dead.  This is probably Momoa’s best episode.  On a side note, I like how Sheppard lies about how many Wraith he killed as compared to Teyla.

Season 3, Episode 5 – Aired: 8/11/2006 – Progeny

Dr. Weir accompanies Sheppard’s team on a mission to an advanced civilization with a past history with Atlantis. They uncover a connection to an earlier discovery in the city.

Season 3, Episode 6 – Aired: 8/18/2006 – The Real World

Dr. Weir awakes in a sanitarium outside Washington, D.C., and is told that Atlantis and the Stargate program exist only in her mind.

This is a somewhat tiresome scenario that continues a trend among genre shows: taking the protagonist and depositing them in some kind of fantasy world where they’re locked up in an insane asylum and their real life is just an illusion in their mind.  I’ve seen it on both Buffy and Smallville as well.  The circumstances as to how Weir ends up this way, Replicator nanites, will have an impact on her fate in the show later in this season.

Season 3, Episode 7 – Aired: 8/25/2006 – Common Ground

John Sheppard is captured by the evil Kolya of the Genii and imprisoned in a cell adjacent to a Wraith as Dr. Weir negotiates for his release.

Pivotal episode that introduces the other great Wraith villain to the show: Todd.  Sheppard is captured by Kolya and the Genii, who torture him in front of his comrades by video link by letting Todd feed on him several times, steadily aging him to an old man.  Sheppard and Todd strike up the first of what will be many uneasy alliances in order to escape and a crucial secret about the Wraith are revealed here.  Not only can the Wraith suck the life out of humans, they can also restore it.

Season 3, Episode 8 – Aired: 9/8/2006 – McKay and Mrs. Miller

When his sister Jeannie comes up with a vital mathematical proof, Rodney returns to Earth to take her back with him to Atlantis. But things become complicated when another Rodney McKay from a parallel universe arrives.

Good episode that introduces Hewlett’s real life sister, Kate, as McKay’s sister, Jeannie, on the show.  You get to learn a lot about McKay’s family life here, particularly that he and his sister have been estranged for years and Rodney hasn’t exactly been the best brother.  Then you also get to see a completely different McKay when a mathematical proof that Jeannie wrote allows an experiment to generate power from another dimension to proceed and leads a McKay from that dimension to cross over in order to get Atlantis to stop the experiment.  The Rodney of our dimension becomes dejected and uneasy when the other McKay is much cooler and seems to be fitting in much better than he does.  We’ll see the other McKay in the next to last episode, Vegas, in Season 5.  Very interesting tidbit and a source of neverending humiliation for McKay is his real first name: Meredith, by which Jeannie prefers to refer to him.

Season 3, Episode 9 – Aired: 9/15/2006 – Phantoms

Sheppard and Ronon find themselves under the influence of a Wraith mind-altering device that threatens to force the entire team to kill–each other!

Season 3, Episode 10 – Aired: 9/22/2006 – The Return (1)

While testing a chain of Stargates that will allow travel from Atlantis to Earth in about 30 minutes (the “McKay-Carter Intergalactic Gate Bridge”), McKay, Sheppard and the team discover an Ancient ship traveling at almost the speed of light.  When Dr. Weir talks to the travelers, she is surprised by their request that the expedition members vacate the city of Atlantis.

Season 3, Episode 11 – Aired: 4/13/2007 – The Return (2)

Major General Jack O’Neill’s mission to defend Atlantis fails as he and Richard Woolsey are taken prisoner during a Replicator assault on the city. Sheppard’s team, Dr. Weir and Dr. Carson steal a Jumper from Stargate Command on Earth and come back to Pegasus galaxy with a plan to retake Atlantis.

Interesting two-parter that features guest spots by Richard Dean Anderson and Robert Picardo.  With the return of the Ancients to Atlantis, the expedition has to abandon the city and return to Earth.  Among those having difficulty with that turn of events is Weir, who has become lackadaisical and self-pitying.  But when the Atlanteans are wiped out by the Replicators, their own creations, it’s up to Weir to suck it up and return with Sheppard and the others to rescue O’Neill and Richard Woolsey. 

Season 3, Episode 12 – Aired: 4/20/2007 – Echoes

The whales of Lantea congregate around the city and the inhabitants of Atlantis begin to suffer ill effects. Are they there to communicate or attack?

Season 3, Episode 13 – Aired: 4/27/2007 – Irresponsible

While investigating reports of a “superhero” on another planet, Colonel Sheppard’s team comes across two old acquaintances.

Whimsical episode that features the return of Richard Kind as Lucius, who previously enraptured the Atlantis crew with a device that made him irresistible.  Now he has an ancient personal shield that makes him invulnerable, which he’s using to con a village into thinking he’s a superhero.  But when Kolya and the Genii show up, he finds he’s not nearly as super as he thought.  Also features the final showdown between Sheppard and Kolya.

Season 3, Episode 14 – Aired: 5/4/2007 – Tao of Rodney

While shutting down unnecessary systems in Atlantis, McKay is zapped by a strange Ancient machine. He begins to have superpowers, but things are never as they seem, and Rodney and the team must race against his mutations to save his life.

This is one of the best episodes of the season that is the other side of the coin to the Season 5 episode, The Shrine, that features an unusual event happening to Rodney that threatens his life and humbles him.  In this instance, the machine that zaps Rodney is artificially evolving his mind to the point where he will ascend.  But it’s a one-way trip so that if he doesn’t ascend, he’ll die.  Since he doesn’t believe that he has what it takes to ascend, this leads him to become more apologetic for the person he’s been to his comrades before the inevitable.  He softens considerably to both Teyla and Ronon, going so far as to heal the scars on Ronon’s back from when he was a runner and had to have a Wraith tracking device removed.  Great work by Hewlett in this episode.  He will end up going in the other direction in The Shrine, where, instead of becoming super smart, he becomes dumber as an alien parasite attacks his brain.  Great exchange between McKay and Ronon in this episode.  McKay, whose appetite has also increased, keeps eating donuts.  McKay: “You could be my sidekick.  Batman and Ronon, it has a ring to it.”  Ronon: You keep eating like that it’ll be Fatman and Ronon.”

Season 3, Episode 15 – Aired: 5/11/2007 – The Game

To while away the hours, Sheppard and McKay have been secretly competing against one another in a real-time strategy game they discovered on Atlantis. To their surprise, they discover that this is more than just a game….

Cautionary episode about game playing gone awry when Sheppard and McKay find out the game that’s similar to the Sims that they’ve been playing is actually taking place on another planet.

Season 3, Episode 16 – Aired: 5/18/2007 – The Ark

The Atlantis team uncovers the last survivors of a civilization who have been placed in suspended animation aboard a space station. As some of the people awaken, problems from the past threaten to destroy everyone on the station, including Sheppard.

Season 3, Episode 17 – Aired: 6/1/2007 – Sunday

The team tries to relax during a mandatory day off until the city and the Expedition are devastated by explosions.

This episode is good, but it also pissed me off, because it concerns the death of Dr. Beckett.  When he discovers that an Ancient device is generating explosive tumors in people (yeah I know, but go with me on this), he refuses to abandon a crewman who has one about to detonate.  This decision costs him his life.  Then the rest of the expedition have to come to terms with their loss, particularly McKay.  It’s a heroic sendoff for Beckett, but when fans such as me didn’t want to see him go, it was bittersweet.  Heart-wrenching episode.  This eventually led to an actual protest by fans outside the production offices of the show.

Season 3, Episode 18 – Aired: 6/8/2007 – Submersion

The team goes searching for an alternate power source beneath the surface of the Lantean ocean. When arriving at the power plant, Teyla senses a Wraith nearby.

Season 3, Episode 19 – Aired: 6/15/2007 – Vengeance

When Atlantis loses contact with the Taranian settlement Sheppard’s team goes to investigate and finds that Michael has been doing experiments on them involving the Iratus bug.

The return of Michael, this time making Wraith bug monsters out of the people who were the survivors from the planet with the supervolcano, including (gasp) Brandy Ledford’s character (although she’s not seen in the episode).  Shitty ending for them.  Interesting turn for Michael, which sets up later Wraith hybrid experiments which will devastate the Pegasus galaxy.
 
Season 3, Episode 20 – Aired: 6/22/2007 – First Strike (1)

Colonel Abe Ellis arrives at Atlantis with a new Earth ship, The Apollo and a new mission. Dr. Weir has misgivings about that mission, one that could start a war with a very powerful enemy. When his mission goes wrong, Weir must take radical action to save Atlantis.

Tense season finale where Atlantis takes a preemptive strike on the Replicators, who, they discover, are preparing war ships.  A tactical nuclear strike on the Replicator planet leads to an interesting retaliation.  The Replicators are directing a powerful energy beam through a Stargate in a shielded satellite that will continuously fire until it drains Atlantis’ shield and destroys the city.  The solution by the expedition is to first sink the city.  When that proves ineffective, they have to move the city by firing up the star drive.  But a plan to use an asteroid to deflect the Replicator beam long enough for the city to escape the planet’s gravity goes awry and the city takes heavy damage when the beam pierces the shield.  Among those critically injured is Weir, with a severe brain hemorrhage.  The city then ends up in a void when the power levels from the ZPM drop to critical levels, leaving them adrift in space with a failing shield.

Season 2 continued the momentum of the show nicely and featured a major addition to the cast in the form of Jason Momoa as Ronon.  I think this was easily the best change in the entirety of Atlantis‘ run, as Ronon was a much more layered and interesting character than Ford, providing the show with new angles to explore by utilizing him than they would have had otherwise.  Season 2 also saw the introduction of Michael, one of the two best villains on the show.

Season 2, Episode 1 – Aired: 7/15/2005 – The Siege (3)

Earth’s new battle cruiser Daedalus arrives under the command of Colonel Caldwell and saves Major Sheppard from his suicide run on the Wraith Hive ships. McKay and his team must get the new ZPM installed and raise the city shields to protect Atlantis before the rest of the Wraith fleet arrive to take the city.

This was the conclusion to the three-part episode.  One of the story threads to emerge from this arc is that Lt. Ford was infected by a Wraith enzyme while a Wraith soldier was feeding on him.  The side effect of the process is that the enzyme infused Ford with enhanced strength and endurance, but it also made him addicted to it and paranoid to the point where he went AWOL, leaving Atlantis (and Sun Francks the show as a regular character).  Sheppard also got a bit of closure on his regret that he couldn’t save Col. Sumner in the pilot when Sumner was being fed upon by a Wraith.  Sumner’s friend and Sheppard’s new commander, Col. Everett, also was fed upon partially, leaving him an older man. 

Everett initially had the same misgivings about Sheppard’s record of disobeying the chain of command back in Afghanistan that Sumner had and he didn’t like Sheppard as Sumner initially didn’t.  he even resented Sheppard for killing his friend  But when Everett had the same fate befall him, he tells Sheppard he wishes he could have been there for him like he was there for Sumner.  The episode also introduces Mitch Pileggi in his recurring role as Col. Steven Caldwell, commander of the Daedalus, the newest ship in the Earth fleet.  Great three-episode arc with plenty of action on multiple fonts.

Season 2, Episode 2 – Aired: 7/22/2005 – The Intruder

Daedalus is infected by a Wraith computer virus. Dr McKay and his team must stop it as members of the Atlantis expedition return from Earth after a meeting at the SGC thanks to the ZPM. During the meeting at the SGC, Dr. Weir learns that the Pentagon plans to replace Major Sheppard with Colonel Caldwell.

Good “ghost in the machine” type of episode as the Wraith virus causes a lot of havoc on board the Daedalus, including killing a couple of crewmen.  This episode also has ramifications for Weir and Sheppard, negative and positive respectively.  The IOA questions Weir’s leadership of the expedition, even as she goes to bat for Sheppard, leading to his promotion to Lt. Col.  This isn’t the last run-in that Weir will have with the IOA, nor the last challenge to her leadership of the expedition.

Season 2, Episode 3 – Aired: 7/29/2005 – Runner

Sheppard and his team attempt to locate Lieutenant Ford, only to find themselves held captive by a young man who is being hunted by the Wraith.

This is not only a pivotal episode for introducing Ronon Dex, but it’s another solid action episode that continues Ford’s arc as well.  Jason Momoa had Ronon’s character down from the beginning and became a great addition to the show.  This is a good episode for Rodney, who is insistent on wearing a hazmat suit due to the high instance of solar radiation on the planet.  Ronon and Ford have a great knife fight in the climax that shows just how much of a badass Ronon really is.  

Season 2, Episode 4 – Aired: 8/5/2005 – Duet

After McKay and Lt. Laura Cadman are culled by a Wraith dart, Sheppard’s team shoots it down. After attempting to re-materialize the pair, Lt. Cadman’s mind ends up sharing McKay’s body.

Good, quirky episode for McKay.

Season 2, Episode 5 – Aired: 8/12/2005 – Condemned

Sheppard’s team discovers a planet untouched by the Wraith because the government sends their criminals to a penal island for the Wraith to feed upon. Sheppard’s Jumper is shot down and crashes on the island.

Season 2, Episode 6 – Aired: 8/19/2005 – Trinity

Ronon Dex discovers that a small number of his people survived the Wraith attack on his planet, including his former military trainer, with whom he has unfinished business. Meanwhile, McKay puts Atlantis at risk when he tries to unlock the secrets of an Ancient power source.

This is a split narrative episode, where Ronon and Teyla get to know each other better.  This is especially so when Ronon has some unfinished business with his former Satedan commander.  Meanwhile, Rodney’s ego at trying to make an Ancient power device work ends up destroying a solar system.

Season 2, Episode 7 – Aired: 8/26/2005 – Instinct

During a mission, Sheppard and his team learn that a lone Wraith — whose dart had crashed leaving him unable to get to the spacegate — has been terrorizing a village for some ten years. They offer to help, but soon after they begin to hunt, Teyla senses that something is different about this Wraith.

Season 2, Episode 8 – Aired: 9/9/2005 – Conversion

After being infected by a retrovirus, Sheppard’s body begins mutating into something insect-like. Beckett and the team race to find a cure before the mutation has gone too far.

Instinct and “Conversion are a de facto two-part episode, the first where Sheppard’s team comes across a young Wraith girl who has an unusual protector in the form of a human.  It also introduces a retrovirus that Beckett had been working on to reverse Wraith DNA, but ends up having the inverse effect, turning the somewhat docile Wraith girl into a full on monster.  Sheppard gets some of the same treatment in Conversion when he becomes infected with the retrovirus and begins mutating into a Wraith monster.  This is a good The Fly episode for Flanigan.

Season 2, Episode 9 – Aired: 9/23/2005 – Aurora

The team finds a large Ancient Ship called Aurora adrift on the edge of the galaxy and it still has Ancients living on board.
 
Season 2, Episode 10 – Aired: 9/23/2005 – The Lost Boys (1)

The team is captured by Lt. Ford, who is now leading a renegade band that is taking the Wraith enzyme. He tries to get Sheppard and the team to help him take out a Wraith hive ship.

Season 2, Episode 11 – Aired: 1/6/2006 – The Hive (2)

McKay attempts to rescue Sheppard, Teyla and Ronon from the Wraith hive ship that Ford wanted to sabotage and destroy.

Another great action-filled two-parter that rounds out Ford’s arc permanently on the show.  Still affected mentally by the Wraith enzyme, Ford has been staging commando raids on the Wraith, harvesting the enzyme from them.  He’s gathered a group of men and has juiced them on the enzyme as well.  When he captures Sheppard’s team, he does the same with them.  Ronon and Teyla feel the effects and their considerable natural fighting skills are heightened even more by the enzyme.  Rodney has his typical reaction to being drugged against his will: he freaks.  The second episode features an assault on a Wraith hive ship in which Ford apparently doesn’t survive.  He isn’t seen on the show afterwards.  

Season 2, Episode 12 – Aired: 1/13/2006 – Epiphany

Colonel Sheppard is separated from his team while investigating an Ancient device; he finds himself in a domain where time is dilated, progressing faster than normal. Doctor McKay frantically looks for a way to save Sheppard before time runs out!

Season 2, Episode 13 – Aired: 1/20/2006 – Critical Mass

SGC discover that The Trust has placed a bomb in Atlantis that will go off when Atlantis dials Earth. Daedalus must warn Atlantis and the team must find the traitor in their midst.

Season 2, Episode 14 – Aired: 1/27/2006 – Grace Under Pressure

Dr. McKay is trapped underwater in a sinking Puddle Jumper and he must rely on Samantha Carter for his survival.

This is an entertaining Rodney-centric episode where he has lengthy discussion with Col. Carter, who isn’t really there, in order to try to cope with his situation.  Rodney knows she’s just a figment of his imagination, but that doesn’t stop him from revealing deep emotions he has for Sam.  Good guest spot by Amanda Tapping.

Season 2, Episode 15 – Aired: 2/3/2006 – The Tower

The team discovers an exact replica of Atlantis on a planet they are exploring. The planet is protected by The Protector who uses the technology to keep the villagers in line and the Wraith away. The Protector is dying and Sheppard is caught up in a dispute among the heirs of the throne.

Season 2, Episode 16 – Aired: 2/10/2006 – The Long Goodbye

Alien combatants look to settle an ancient score by using Weir and Sheppard as pawns.

An interesting Return To Tomorrow-styled episode (Star Trek) where Weir and Sheppard have their bodies taken over by two aliens who have unfinished business which each other: namely, they want to kill each other.  Weir finally gets to see some real action, even if it’s not really Weir.

Season 2, Episode 17 – Aired: 2/17/2006 – Coup D’etat

When the Atlantis team finds out that the Genii have grown into a new menace, they realize that the armistice with their old enemy may soon come to an end.

Season 2, Episode 18 – Aired: 2/24/2006 – Michael

Lieutenant Michael Kenmore, suffering amnesia, suspects that Atlantis personnel are lying to him about what actually happened to him on his last mission against the Wraith.

One of the best episodes of the season and one which introduces a key Atlantis villain, Michael (Connor Trinneer).  You know something’s off about the way Weir and the others are treating this soldier who’s new to Atlantis and who suffered amnesia from a Wraith attack.  And you wonder why the hell Ronon wants to kill him so badly.  When the truth about Michael is revealed, it raises an interesting moral dilemma about just how far is too far in the Atlanteans’ efforts to prevail over the Wraith.  Teyla gets a lot of good screen time with Michael this episode.  Michael returns several times to become one of the most dangerous enemies the expedition will encounter, and he’s one that they created.  

Season 2, Episode 19 – Aired: 3/3/2006 – Inferno