The Siege: Part 3
Season 2, Episode 1 TV-PG
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Rescued from a near-fatal encounter with the Wraith, Lt. Aiden Ford (Rainbow Sun Francks) receives medical care at the Atlantis base. However, his abnormally quick recovery leads Dr. Beckett (Paul McGillion) to worry that the Wraith who attacked Ford may have injected him with a harmful enzyme, causing long-term and unpredictable damage.
Meanwhile, as the Wraith’s siege of Atlantis rages on, Sheppard (Joe Flanigan) finds himself surrounded by the enemy. He is rescued by the timely arrival of Colonel Steven Caldwell (Mitch Pileggi), commander of the Daedalus. Launched from Earth and sent in to assist the Atlantis team during battle, the Daedalus helps to defeat the Wraith’s first wave assault on the city.
Their relief is short-lived, however. The team soon learns that the Wraith are planning the next wave of their onslaught -- an entire fleet is about to descend on the city. With a little over a day before the assault, Dr. Weir (Torri Higginson) realizes that the Daedalus will not be enough to fight the Wraith's forces. McKay (David Hewlett) devises a drastic plan – but there may not be enough time to perfect the complicated technology his plan requires before the Wraith arrive.
Intruder
Season 2, Episode 2 TV-PG
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When a scientist is killed in the Daedalus' computer room, McKay (David Hewlett) first believes the poor circuitry is at fault. However, when another scientist is killed while investigating the death, McKay begins to suspect that someone – or something – is deliberately planning these breakdowns.
Soon after, McKay is alerted to a virus on one of the ship's computers. When he runs its code through a translator, he is shocked to discover that it is written in Wraith. Even worse, he learns that the virus has the ability to re-write itself, making it seemingly impossible to conquer. Realizing that the program’s capability to mutate has virtually given it a mind of its own, McKay worries that the Wraith may use the virus to take control of the ship – with potentially deadly results.
As feared, the virus’ artificial intelligence soon takes control of the Daedalus’ auxiliary ships, and the crew becomes increasingly powerless to defend themselves. Fearing that the Wraith will use the Daedalus' advanced features to attack Atlantis, McKay and Sheppard (Joe Flanigan) race against the clock to counteract the virus before the Wraith turn the Daedalus’ advanced technology against the city.
Runner
Season 2, Episode 3 TV-PG
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When a routine, off-world science mission comes across a mutilated Wraith carcass, the team suspects Ford may be involved. Intrigued, they split into teams to investigate. Teyla (Rachel Luttrell) and Sheppard (Joe Flanigan) encounter Ronon Dex (Jason Momoa), a fierce warrior who survived a battle with a Wraith seven years earlier and has been on the run ever since.
When Dex reveals to Teyla and Sheppard that Ford (Rainbow Sun Francks) has taken up residence on the planet, they enlist his help to locate their friend. The duo hope to rehabilitate Ford to his former state.
McKay (David Hewlett) eventually stumbles upon the increasingly incoherent and maniacal Ford, and tries to reason with his former colleague and friend. However, McKay begins to see how far gone Ford has become -- addicted to the enzyme injected in him by the Wraith who attacked him, Ford has been brutally killing Wraith to get a fix of the solvent. Reluctantly, McKay and the rest of the crew must face the realization that they may never be able to save Ford from what he has become.
Duet
Season 2, Episode 4 TV-PG
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During an investigation of a planet leveled by a Wraith attack, McKay (David Hewlett) and new security team member Lt. Laura Cadman (Jamie Ray Newman) are transported aboard a Wraith Dart, which subsequently crashes. Unfamiliar with the Wraith technology, Atlantis scientist Dr. Zalenka (David Nykl) is only able to transport McKay out of the rubble. Cadman’s body is nowhere to be found. Zalenka believes that she is still trapped inside the Dart, until McKay claims to hear her voice – coming from inside his own head! It seems that Zalenka's experiment, rather than saving the two separately, caused them to unite – and Cadman must remain inside of McKay's head until Zalenka can figure out a way to separate the pair.
Meanwhile, as Ronon Dex (Jason Momoa) settles in at Atlantis, he shows off his impeccable fighting skills during arsenal training. Impressed, Sheppard (Joe Flanigan) implores Weir (Torri Higginson) to put aside her reservations about the newcomer and consider allowing Ronan to join the Stargate Atlantis team.
Condemned
Season 2, Episode 5 TV-PG
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When the Atlantis team sets out to a distant planet, they land on a small island off the main coast and are attacked by a group of savages. Barely escaping the island with their lives, the team is rescued by one of the planet's security vessels and brought to the considerably more civilized mainland.
Once safely on shore, the team learns that the island had been set aside for the banishment of prisoners and is susceptible to Wraith attacks. The rest of the planet, however, is immune to such Wraith assaults. Intrigued by this, as well as by the planet's unconventional energy source, the team tells Weir (Torri Higginson) of their discovery. However, when Weir arrives on the planet to investigate further, she begins to suspect that the mainland's idyllic environment may be the result of a sinister pact between the planet's leader and the Wraith.
Trinity
Season 2, Episode 6 TV-PG
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While doing standard recon on a planet thought to have been destroyed by the Wraith long ago, the team finds an Ancient structure standing intact amidst the ruins. After some investigating, they discover that the monolith served as a military research facility where the Ancients worked to develop an advanced method of harnessing energy. When the Wraith attacked before the project could be completed, the underdeveloped technology malfunctioned and destroyed the civilization.
McKay (David Hewlett) theorizes that if the powerful technology is fully developed, it could serve as a potent source of energy for Atlantis. Hope turns to fear, however, when McKay's first attempt at reviving the energy source results in the death of one of the Atlantis scientists.
Despite the team's apprehension, a determined McKay insists on moving forward with finishing the project. But can McKay unravel the intricacies of the Ancients' technology without putting himself and Sheppard in mortal danger?
Instinct
Season 2, Episode 7 TV-PG
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During a visit to a distant planet, the team discovers a village whose inhabitants live in fear of a Wraith residing in their midst. When the team sets out to confront the creature, they encounter Zaddik (John Innes), a scientist who has been living with Ellia (Jewel Staite), a Wraith child, for the past several years. Zaddik has developed a serum that works to satiate the young Wraith's appetitie and prevent her from feeding on him.
Dr. Beckett (Paul McGillion) is intrigued by the serum, having been eager to test an experimental retrovirus of his own that could give the Wraith humanlike qualities and rid them of their predatory instinct. Beckett meets with Zaddik and his supposedly tame Wraith companion, hoping he can begin a controlled experiment on Ellia. However, when Ellia downs his retrovirus, the underdeveloped formula has the opposite of the desired effect.
Conversion
Season 2, Episode 8 TV-PG
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Within hours following his encounter with the mutated Wraith child Ellia (Jewel Staite), Sheppard (Joe Flanigan) is shocked to find that his wounds have disappeared without a trace. Soon after, he begins exhibiting other symptoms similar to the ones that plagued Ford following his own Wraith attack.
Dr. Beckett (Paul McGillion), realizes that a small amount of the retrovirus that Ellia ingested is now in Sheppard's bloodstream - and he is quickly mutating into the very creature that attacked him. As Sheppard becomes less lucid by the hour, the team races against the clock to save his life and reverst he effects of the retrovirus.
Aurora
Season 2, Episode 9 TV-PG
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When Atlantis's deep-space sensors detect the Aurora, an ancient Atlantian warship, at the edge of the galaxy, Sheppard's team wastes no time hitching a ride to it aboard the Daedalus. Upon their arrival, they encounter a Wraith scout ship. They destroy the scout before it can cause trouble — or so they hope.
Sheppard leads his team onto the derelict warship, where they discover hundreds of crewmembers frozen in stasis pods. Although technically alive, the Atlantians are
thousands of years old, and their aged bodies can't survive the defrosting process. Still, there might be a way to talk to them: McKay discovers that all the pods are linked by an
active neural interface, allowing the crew to coexist with each other in a virtual environment.
The Lost Boys
Season 2, Episode 10 TV-PG
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While exploring a new planet, Sheppard, McKay, Teyla and Ronon are ambushed by a group of men armed with Wraith stunners. They awaken to find themselves prisoners in a cave, where they discover the mastermind behind the attack: Lt. Aiden Ford.
Ford was last seen being captured by a Wraith dart after overdosing on a powerful Wraith enzyme. Now, Ford invites his former teammates to enjoy a meal while he tells them how his enzyme-enhanced abilities allowed him to escape. Since that time, he has recruited a group of followers, all of whom are willingly addicted to the drug.
To the team's horror, Ford then announces that their meals are laced with the enzyme. Determined to prove that the enzyme is both safe and useful, Ford intends Sheppard's team to be his living evidence, and the expects Sheppard, who remains free of the drug, to be his witness.
The Hive
Season 2, Episode 11 TV-PG
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Captured by the Wraith, Sheppard (Joe Flanigan), Teyla (Rachel Luttrell), Ronon (Jason Momoa) and Ford (Rainbow Sun Francks) are being held hostage aboard a hive ship. As the team desperately searches for some means of escape, they are shocked to discover a coalition of Wraith followers on board the ship.
McKay, who is still stranded on Ford's planet, soon realizes that the team has been captured. In order to escape the planet, he comes up with an unconventional plan: he injects himself with a massive amount of the dangerous Wraith enzyme. The drug provides him with brute strength, and after knocking the guards that surround him unconscious, he is able to dial the gate and leave the planet. When he arrives on Atlantis completely incoherent, Dr. Weir (Torri Higginson) and Dr. Beckett (Paul McGillion) put him under immediate medical supervision.
Once recovered, McKay is able to calculate the location of the ship upon which the team is stranded. As tensions rise on the hive ship between the Wraith and the Atlantis team, he and Caldwell (Mitch Pileggi) must devise a plan to bring the rest of their team to safety.
Epiphany
Season 2, Episode 12 TV-PG
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After detecting an energy spike over a forested area on a distant planet, the Atlantis team decides to investigate. Their travels lead them to a portal built into a rock wall with Ancient carvings and a portal built into it. Intrigued, Sheppard decides to test the portal to see where it leads, and before he can stop himself, is pulled through to the other side with no way to get back or communicate with the team.
When no rescue team comes through the portal, Sheppard explores his surroundings and he encounters Avrid (David McNally), a man on the run from a dangerous creature. After a violent showdown, Sheppard succeeds in warding off the creature. Avrid then brings the injured Sheppard back to his home to recover. There, Sheppard discovers that all the inhabitants of the planet are direct descendants of the Ancients, and he is the only one ever to have survived such an attack.
Meanwhile, the rest of the Atlantis team is trying to figure out what happened to him. After translating the writing on the rock with the help of some Ancient textbooks, Weir (Torri Higginson) discovers that Sheppard has been transported into a time dilation field, designed by the last of the Ancients as a sanctuary from the Wraith - a place where people could live in peace and safety and ascend to a higher plane of existence. However, there are also a warning inscribed on the stone: once the threshold across the portal is crossed, there is no return.
Critical Mass
Season 2, Episode 13 TV-PG
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General Landry (Beau Bridges) informs the team that the Goa'uld have planted a bomb on Atlantis and will be triggered by any attempt to dial the gate. After some investigation, McKay (David Hewlett) determines that the failsafe mechanism on Atlantis' energy source hase been disabled - so any action that might cause it to overload (such as dialing the gate) would result in an explosion. Furthermore, the mechanism is now locked with an unbreakable code, and they must find the individual who tampered with it in order to enable it once again.
To make matters worse, two Wraith cruisers are headed straight for Atlantis. They must activate the cloak in order to keep the city invisible to the Wraith - but such an operation would surely cause the energy source to detonate. With time running out, an alarmed Weir (Torri Higginson) launches a full-scale investigation to find the saoteur. She is shocked when she discovers that the perpetrator is a member of her own team.
Grace Under Pressure
Season 2, Episode 14 TV-PG
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On a puddle jumpter test flight, McKay (David Hewlett) and a pilot suddenly lose control of the ship and crash into the ocean. Though he is able to communicate with Weir (Torri Higginson), he soon loses contact with Atlantis as he sinks lower and lower.
Trapped in the back of the ship with almost no power and a badd concussion, McKay begins to hallucinate. Fortunately for him, his hallucinations come in the form of his intellectual rival, Samantha Carter (Amanda Tapping), who is ready to assist him in finding a way out. However, before they have time to formulate a plan,t he jumper descends to the ocean floor, and the impact causes a small break in the ship's hull, allowing water to sink in.
Meanwhile, back on Atlantis, Weir and Sheppard have located McKay and devise a plan to rescue him - but will they reach him before time runs out?
The Tower
Season 2, Episode 15 TV-PG
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During a trade mission on a distant planet, the team is introduced to a village with a central tower - one almost identical to the central spire of Atlantis - inhabited by the village's revered leader, who is able to protect the people that live there from the Wraith.
Intrigued, the team inquires about meeting this Lord Protector, but the overly suspicious guards surrounding the tower capture Sheppard (Joe Flanigan) and confiscate the others' weapons. Inside the tower, Sheppard is introduced to the dying Lord. When the Lord and his advisors discover that Sheppard also possesses the Ancient gene needed to protect the village, they decide that he should marry into the family and become the Lord's successor.
While McKay (David Hewlett) investigates the source of the Protector's power, the Atlantis team tries to free the people from this unjust ruling family, but is unwittingly caught up in a devious power play.
The Long Goodbye
Season 2, Episode 16 TV-PG
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On the way to investigate a potential source of energy, the team encounters two pods in orbit around a moon. They decide to take one back to Atlantis for observation. Upon opening the pod, they find a woman in stasis. As they speculate about her age, an energy beam emanates from the pod and hits Weir (Torri Higginson), allowing her to harbor the consciousness of the woman inside the pod.
Through Weir, the team learns that the woman, Phoebus, was from a race of explorers whose vessel was attacked by the Wraith. She claims that the body of her husband, Thalan, occupies the second of the two pods found by McKay, and her wish is for the team to bring him back to Atlantis so that Sheppard (Joe Flanigan) may harbor the man's consciousness and allow him to communicate one last time with his wife.
Unfortunately, once the plan is put into action, the team learns that it was all a ruse: Phoebus and Thalan were enemies, and her real intent was to have the team revive Thalan so she could finally finish him off. Now, as Phoebus and Thalan wreak havoc throughout Atlantis in the forms of Weir and Sheppard, the rest of the team must find some way to stop them before they destroy each other - and Atlantis itself!
Coup D'etat
Season 2, Episode 17 TV-PG
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When a village on a distant planet is ravaged by fire, the team is called in to investigate the damage. In the attack, Major Lorne, a member of an off-world team working there, has seemingly disappeared. Upon further investigation, Teyla (Rachel Luttrell) and Ronon (Jason Momoa) find a wanted list circulating about the village – and on it is Major Lorne's name – along with those of Sheppard (Joe Flanigan) and McKay (David Hewlett). Weir (Torri Higginson) quickly deduces that whoever composed it was seeking people with the Ancient certain gene that provides the ability to operate Ancient technology, including Ancient ships. Compounding matters, the team is contacted by Ladon Radim, a former Genii. Now
claiming to have severed ties with Atlantis' old foe, Ladon has an offer: a valuable zero point module in exchange for their help in planning a coup against the Genii. Ladon claims the Genii have been harboring nuclear weapons and are becoming an even greater threat. Skeptical of what they've been told, the team decides to alert Cowen, the Genii leader, of
Ladon's plans. Cowen confirms that Ladon is no longer linked with the Genii, and thanks the men for the warning. Satisfied that the Genii pose no immediate threat, Sheppard and McKay plan a raid to simply "appropriate" the ZPM from Ladon. However, when they arrive, their team is taken hostage by Ladon and Cowen, who are, after all, still Genii accomplices. Their plan is to negotiate for Atlantis' Jumper ships which they intend to use to attack the Wraith. Now, Weir must negotiate with the Genii – before it's too late.
Michael
Season 2, Episode 18 TV-PG
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Lt. Michael Kenmore awakens in Atlantis' infirmary with no memory of how he got there — or who he is. Dr. Weir, Col. Sheppard and Dr. Beckett explain that he's a member of the expedition's military contingent who was captured by the Wraith during a dangerous mission. Although Sheppard's team rescued him, he was badly injured and has been unconscious for days.
Michael explores Atlantis, but even his personal quarters awaken no memories of his prior life. Instead, he notices that he can read and understand a Wraith schematic that Dr. McKay is studying. As if that's not unsettling enough, McKay's nervousness, Teyla's kind but evasive friendliness, and Ronon's obviously heartfelt desire to break his neck all force Michael to believe that there's much more to his story than anyone's letting on. Unnerved, he visits Dr. Heightmeyer, Atlantis's psychiatrist, who assures him that everything will be fine. But that night, Michael has a nightmare. He dreams he's a Wraith.
Teyla struggles to reassure him, but Michael becomes convinced that the Wraith manipulated his mind while he was their prisoner. Certain that the Atlantis team knows more than they're saying, he secretly searches Beckett's files and uncovers recordings from security cameras showing his treatment. There, he finally discovers his real identity: Though he's a man now, on the day he arrived, he was a Wraith.
His new knowledge forces the others to drop their act and tell him the truth. Michael was a Wraith warrior until Sheppard's team captured him and Dr. Beckett gave him an experimental drug therapy designed to turn Wraith into humans. Michael's anger at this news ignites his dangerous, barely suppressed Wraith instincts. As Ronon and a security contingent escort him to the infirmary for another treatment, he fights free of them and, before he's recaptured, kills a guard. Consequently, he's transferred under high security to the expedition's new Alpha site, a secondary base on another planet where Dr. Beckett can continue the experiment with less risk.
Beckett and Teyla both feel moral qualms about their actions — especially Teyla, who stays by Michael's side, convinced that he's good at heart. Her trust is put to the test, however, when he manages to break loose and escape with her as his hostage. Her life may now depend on Michael's human compassion — if, that is, he actually has any.
Inferno
Season 2, Episode 19 TV-PG
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Sheppard's team visits the planet Taranis at the invitation of two leading citizens, Dr. Norina Pero and Chancellor Lycus, who want McKay to repair a failing shield generator at an Ancient base they've discovered. Lycus also shows the team a massive Ancient warship, much like the Aurora, hidden in a vast warren of tunnels beneath the base. Although the warship is damaged and currently inoperable, Dr. Weir eagerly opens trade negotiations with Lycus as soon as she learns of its existence.
As mysterious earthquakes rattle everyone's nerves, McKay overcomes his attraction to Dr. Pero long enough to discover that her people have seriously overtaxed the shield's capabilities. Worse, the shield's energy source is the magma chamber of a supervolcano beneath the base — a volcano that has been destabilized by the excessive energy demands. A catastrophic eruption is now imminent: Half the continent is about to be ripped apart, rendering the entire planet uninhabitable. Everyone must evacuate.
As the earthquakes grow stronger, local villagers begin arriving at the base through the relative safety of the Ancient tunnels. Weir and Lycus lead some of them through the stargate to Atlantis, but seconds later, the ground around the 'gate erupts. The stargate sinks forever into a pool of molten rock.
From Atlantis, Weir immediately dispatches the Daedalus to Taranis, but it will require multiple trips to evacuate everyone. Sheppard and McKay, knowing that they don't have that much time, start repairing the Ancient warship while Teyla, Ronon, and Dr. Beckett hurry to a nearby settlement, to organize the first group of evacuees.
Soon after the Daedalus departs from Taranis, new vents erupt, ash starts falling, and the outside air turns toxic, forcing Beckett, Teyla and Ronon to send the remaining villagers through the tunnels to the warship. Then McKay discovers that a lava flow has sealed the main hangar doors shut. Now, even if he can repair the ship, they'll still have to find a way past this molten barrier.
Teyla and Ronon remain in the settlement until they've rounded up the very last of the villagers, only to be trapped when the tunnel that leads to the base collapses. As the duo fights to stay conscious in the deadly air, Sheppard notices that they're missing and descends into the maze of tunnels to find them. Soon he's cut off, too — and even if he somehow makes it back, there's still no guarantee that McKay can even get the warship off the ground.
Allies
Season 2, Episode 20 TV-PG
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A Wraith hive ship arrives in orbit above Atlantis. In the cloaked city below, everyone is stunned when Michael radios down with an unnerving request: He wants to negotiate an alliance.
Frustrated in their quest to locate Earth, the Wraith are now running short of their food — humans — and have begun fighting among themselves. For this reason, Michael seeks a weaponized version of Dr. Beckett's anti-Wraith retrovirus, which briefly gave him a human body. He wants to deploy it against rival hives, turning them human and feasting on the results. His hive will gain food and power, and the Atlantis team can deal a fatal blow to thousands of their enemies.
Weir and her senior staff decide that such a payoff is worth the immense risk of trusting the Wraith, and soon the new allies are working side-by-side. With the help of a Wraith scientist, Beckett and Zelenka struggle to weaponize the retrovirus, while McKay coordinates with the hive's crew to practice bypassing a hive ship's defenses.
The Wraith, however, make everyone uneasy. Worse, their first attempt to target another ship with the new weapon ends in disaster: Their enemies discover the canisters of the retrovirus too soon and open fire. Michael's hive ship and the Daedalus barely escape intact.
The imperious Queen of Michael's hive now threatens to reveal Atlantis's existence to all the Wraith if the humans won't design a reliable delivery system for the weapon. McKay, frustrated, demands that she help by allowing him free access to every last piece of information about Wraith ships. To his astonishment, she agrees, downloading a virtual encyclopedia of technical specs to Atlantis's computers.
Zelenka delves into this goldmine of strategic intelligence while McKay — escorted by Ronon — explores the hive itself and discovers a perfect delivery point for the retrovirus in the atmospheric system. With that, they're ready to attempt a second attack: The Daedalus will beam the canister onto another enemy hive. McKay and Ronon will observe from Michael's ship. Sheppard will observe from the Daedalus.
But soon after the mission is underway, Zelenka discovers that the electronic Wraith encyclopedia was infected with a virus of its own — and now that virus is loose in Atlantis's computers. It's too late to warn the Daedalus, which drops out of hyperspace to find itself trapped under a ferocious bombardment from two hives — the enemy vessel and Michael's ship. The alliance was nothing but a ruse; the real plans of the Wraith are far more sinister. Far from giving up on finding Earth, they've just tricked the Atlantis team into giving them exactly the information they need to get there.
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