Rescued from a near-fatal encounter with the Wraith, Lt. Aiden Ford receives medical care at the Atlantis base. However, his abnormally quick recovery leads Dr. Beckett 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 finds himself surrounded by the enemy. He is rescued by the timely arrival of Colonel Steven Caldwell , 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 realizes that the Daedalus will not be enough to fight the Wraith's forces. McKay devises a drastic plan – but there may not be enough time to perfect the complicated technology his plan requires before the Wraith arrive.

During an investigation of a planet leveled by a Wraith attack, McKay and new security team member Lt. Laura Cadman are transported aboard a Wraith Dart, which subsequently crashes. Unfamiliar with the Wraith technology, Atlantis scientist Dr. Zalenka 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 settles in at Atlantis, he shows off his impeccable fighting skills during arsenal training. Impressed, Sheppard implores Weir to put aside her reservations about the newcomer and consider allowing Ronan to join the Stargate Atlantis team.

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 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.

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 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?

On an unexplored planet, Sheppard, McKay, Teyla and Ronon hike into a village at dusk. The startled inhabitants insist that they spend the night. Apparently, after darkness falls, a mysterious killer stalks the area, sucking the life from its victims. Sheppard and his team instantly guess what they're dealing with: a Wraith.Sure enough, a leading villager, Goran, explains that a spaceship crashed near the village ten years ago. Frightened, the villagers tried to kill all the crash survivors, but one survived and began to feed. Two years later, Goran's own son vanished into its clutches. As morning dawns, Sheppard and his team head into the forest to track down the Wraith, but they're in for a surprise. The trail leads into a cave, where a young female Wraith cowers in a candlelit laboratory. She lives there with a human scientist named Zaddik, who begs the team not to kill his "daughter." Zaddik claims that he helped in the massacre ten years ago, but when he found a young Wraith child, he couldn't bear to kill her. Instead, he brought her to this cave, where he has hidden her ever since. He has even developed a serum that he believes allows his adopted daughter, Ellia, to survive without feeding on humans. The two love each other, and they dream of a day when Ellia can be accepted in the village. Sheppard doesn't let down his guard. A Wraith has been killing villagers, and this girl is definitely a Wraith. Still, he brings in Dr. Beckett to test Zaddik's serum. Beckett arrives with an experimental retrovirus that has the potential to remove a Wraith's alien DNA, leaving behind only human genetic material. It's not finished yet, but someday, perhaps Ellia can fulfill her dream of living as a human.While Ellia remains at the cave, another villager is murdered. Forced to conclude that Ellia was not the only Wraith to survive the crash, Sheppard sets out with Teyla and Ronon to hunt down the second Wraith.Unfortunately, Ellia harbors more deadly secrets than anyone guesses. Desperate for acceptance, she risks injecting herself with the retrovirus — without Beckett's permission. The untested drug strips away her human side. With Ellia transformed into a mindless monster, Sheppard's team now must confront two killers

Having been savagely bitten by the Wraith girl Ellia, Sheppard hurries back to Atlantis for medical treatment. Both he and Dr. Beckett are shocked, however, when they realize that the wound has vanished. Sheppard's arm is completely free of any trace of the bite.Beckett starts running tests. While waiting for the results, Sheppard goes on a run with Ronon — and beats him without breaking a sweat. Then Sheppard spars with Teyla, and beats her easily, too. His strangely high spirits overwhelm him and he suddenly kisses a very surprised Teyla — which is when Beckett calls him back to the infirmary.Sheppard has been infected with the Wraith retrovirus that Ellia was carrying. Beckett hopes that the substance will break down harmlessly in Sheppard's body, but he can't be sure. Weir orders Sheppard to stay in Atlantis and report for check-ups every six hours until they have more definitive answers. That night, a strange, scaly patch appears on Sheppard's arm. Dr. Beckett confirms what Sheppard himself already fears: The retrovirus is at work, transforming Sheppard into a mindless Wraith. As Weir reluctantly reassigns Sheppard's duties to Col. Caldwell, Sheppard finds himself confined to the infirmary, facing a doomed struggle to preserve his sanity. Beckett's team devises a risky solution: theoretically, they can inject Sheppard with Iratus bug stem cells programmed with human RNA. The catch is that someone will need to collect live Iratus eggs — and Iratus bugs are lethal killers, just like the Wraith who evolved from them. Sheppard asks Weir to let him lead this dangerous mission. She refuses. In furious frustration, he slams his fist through a glass window — proving, to his dismay, how much self-control he has already lost. Leaving him behind, McKay, Teyla, Ronon and Beckett take a team to the Iratus bug homeworld. There, they venture into a cave to find the creatures' nest. The place is swarming with bugs. As Beckett tries to steal an egg, the bugs attack. Two men are killed before the team can escape — without the eggs. A second attempt is unthinkable.Sheppard's transformation grows worse. In another day, he'll be gone forever. Seeing no hope, his friends struggle to accept defeat — but Sheppard himself might hold the key to his own salvation.

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 crew members 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. Eager to chat with these survivors from the distant past, Sheppard enters an empty stasis pod and McKay connects him to the interface. Sheppard immediately finds himself aboard a fully powered Aurora. To his surprise, the Atlantians there treat him like an intruder and toss him in the brig.The Aurora's captain is intrigued by Sheppard's story, but doesn't remember entering a stasis pod, doesn't believe that his world is a computerized fiction, and certainly isn't convinced that 10,000 years have passed. Instead, he and his single-minded first officer apparently believe that they're still in their own time. They're racing to upgrade their ship's hyperdrive engines so they can reach Atlantis quickly and deliver vital intelligence about a critical weakness in the Wraith's defenses.Back in the real world, the Daedalus's sensors spot two Wraith cruisers heading their way. They'll arrive in just over an hour. Then Ronon and Teyla make an even more chilling discovery: One of the stasis pods contains a Wraith. He has hacked into the neural interface and must be posing as a crewmember within the virtual environment.McKay enters the virtual world and warns Sheppard of the impostor. The two must win the captain's trust and root out the Wraith, and not just to save themselves. After all, by spying on the hyperdrive modifications, the undercover Wraith can learn how to build much faster intergalactic ships. If Sheppard and his team can't stop this virtual espionage, the Wraith will soon be able to travel between galaxies and attack the richest feeding ground of all — Earth.

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 Teyla, McKay and Ronon's 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 he expects Sheppard, who remains free of the drug, to be his witness.Sheppard and his team, of course, immediately try to escape, but Ford has removed vital control crystals from the local stargate's dialing device, rendering it useless. Thus, even though McKay, Teyla and Ronon will soon feel the first effects of drug addiction, they see no choice but to play along with Ford's insanity — for now. To show off the abilities of his men, Ford orders Sheppard and Teyla to accompany a guerrilla team on a raid of a Genii outpost. While Sheppard and Teyla witness the brutish tactics of Ford's men, McKay explores the cave's impressive laboratories. Afterwards, confident that his former teammates are impressed by his accomplishments, Ford reveals that he needs their help with a special mission: the destruction of a Wraith hive ship.He has captured a Wraith dart that can land his strike force on a passing hive ship, allowing them to plant explosives. First, though, McKay must repair the dart, and then Sheppard — the only pilot — must fly it. Sheppard is sure the audacious plan is too risky to succeed, but, hoping to fly the dart back to Atlantis instead, he and McKay cooperate with Ford.Unfortunately, Ford anticipates just such an escape attempt: Immediately before the mission, he orders McKay to remain behind as a hostage, to be killed unless Sheppard obeys his orders. Seeing no more alternatives, Sheppard — with Teyla, Ronon, and Ford's strike team on board — embarks on the mission. He's sure it's doomed ... and he's not wrong.

Captured by the Wraith, Sheppard , Teyla, Ronon and Ford 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 and Dr. Beckett 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 must devise a plan to bring the rest of their team to safety.

On a new planet, Sheppard, McKay, Teyla, and Ronon discover an intriguing portal in a mountainside: an opaque force field surrounded by Ancient text. After inserting a camera through the field to check for danger, Sheppard decides to enter the portal himself. The instant he begins, however, he feels terrible pain. His teammates struggle to pull him back out, but the portal inexorably sucks him through. After Sheppard vanishes, McKay makes a chilling discovery: The camera, which was only inside the portal for a few minutes, recorded hours of footage. Time runs much more quickly on the other side of the barrier; Sheppard could already be starving to death. McKay, Ronon, and Teyla quickly toss all their supplies through the portal. Then McKay departs for Atlantis to get help — before Sheppard dies of old age.Indeed, inside the portal, days have passed. Trapped in a cave without food, water, or word from his team, Sheppard is discouraged. The arrival of the supplies helps, but when more days pass with no further contact, he's forced to seek food elsewhere. He discovers that, on the other side of the immense mountain range above him, the cave opens into a verdant valley. Unexpectedly, a man races up to him, shouting frantically about a beast. Then the beast — a semi-invisible monster — attacks them both, knocking Sheppard unconscious. He awakens in a tranquil village. The man, Avrid, and his sister, Teer, explain that the Ancients created this valley as a place for people to meditate on spiritual truths and, eventually, Ascend to a higher plane of existence. To Sheppard's horror, they add that, except by Ascending, no one can leave the valley. Ever. Weeks turn into months as, with Teer's help, Sheppard struggles to adapt to his new life. Then, one day, the mysterious beast attacks the village. To Sheppard's disgust, the villagers hide, leaving him to face the creature alone. He barely survives. Feeling abandoned by his teammates and now by the passive villagers, the deeply frustrated Sheppard tries to make his new friends understand that Ascension won't mean much if they're mauled to death before they can achieve it. Teer confidently responds that her lifetime of spiritual practice has given her precognitive abilities. She has foreseen that Sheppard will defeat the beast and lead her people to Ascend. Sheppard has serious doubts. He can't defeat the supernatural monster alone, and Ascension isn't really his thing. Luckily, though he doesn't know it, his teammates are on their way — with just one small catch: They could be years too late.

On Earth, a galaxy away from Atlantis, Gen. Landry receives intelligence that The Trust, a group of conspirators controlled by the evil Goa'uld, have learned of the Ancient city and sent an undercover operative there to plant a bomb. Details are sketchy, but any use of Atlantis's stargate to dial Earth will somehow trigger the explosion. The moment that Earth relays this news to Atlantis, Dr. Weir orders both the stargate and the city's main power source, a ZPM, shut down. She also orders the absent starship Daedalus to return, because the bomber might be trying to escape aboard it. In the midst of this intense search for both bomb and bomber, the city's distress beacon activates. Before McKay can shut it off, it catches the attention of two Wraith cruisers, who head straight for Atlantis. If they discover that the city still exists, they will attack immediately. To prevent such a catastrophe, McKay prepares to reconnect the ZPM and use its power to cloak the city from view. Meanwhile, Teyla finds herself occupied with a very different concern. Charin, her beloved adopted grandmother, is seriously ill. Although Charin urges Teyla to accept her death as inevitable, Teyla begs Dr. Beckett to heal her friend. When he explains that he can save Charin's life by installing a pacemaker for her heart, Teyla is elated, but the old woman reiterates her desire to die a natural death and gently orders Teyla to respect her wishes. With the exception of this private grief, suspicion is consuming the city. McKay suspects that Lt. Cadman, a demolitions expert, is the saboteur. Weir suspects Dr. Kavanagh, a disgruntled scientist. For his part, Kavanagh suspects Dr. Zelenka, who is off-world on a conveniently timed mission. Weir's suspicions carry the most weight, however, so the investigation's focus settles on the prickly and defensive Kavanagh. Then McKay discovers that no actual bomb exists. Instead, the saboteur has removed the failsafes from the ZPM, so that it will overload in a massive explosion as soon as it emits any significant amount of power. The saboteur has been trying to provoke them into dialing Earth or cloaking the city — either of which will cause an overload. But the Wraith are closing in. In desperation, McKay shuts down as many secondary systems as possible and activates the cloak. As the power usage levels inch toward critical, Weir considers torturing Kavanagh for answers, and Charin hovers near death. Atlantis teeters on the brink of destruction, though whether it will come from without or from within remains to be seen.

During the first test flight of a Puddle Jumper that Dr. Zelenka has repaired, the small ship abruptly crashes and sinks into Atlantis's ocean with Dr. McKay and the pilot, Griffin, on board. Moments later, mounting water pressure cracks the Jumper's windshield. Griffin sacrifices himself to seal a horrified McKay into the relative safety of the windowless rear compartment, seconds before the windshield gives way. McKay is now utterly alone — and still sinking. He manages to activate an emergency beacon, turn up the heat, and fix the carbon dioxide scrubbers. Every action he takes, however, costs power — power he desperately needs to stay alive. He's already close to panic when a strange whale-like creature starts taking an interest in the Jumper. But the creature's swimming gives McKay an idea. If he can power up the Jumper's drive pods, perhaps they can propel him to the surface. Suddenly, however, an unexpected visitor joins him: Col. Carter, from SG-1. McKay, shocked, accuses her of being a hallucination, and she cheerfully agrees. The concussion he received in the crash, plus the stress he's been under since, has provoked his subconscious to summon this unusual form of help. Unfortunately, McKay and Carter — or McKay and his subconscious — have a fundamental difference of opinion. He believes he must risk activating the drive pods, while Carter argues that this will only waste the last of his precious power. She wants him to remain calm and trust his teammates to rescue him. McKay, by contrast, blames Zelenka for the crash and has no confidence in the Atlantis team's ability to save him — especially without his genius to help them out. As water starts leaking into the Jumper, he insists on pursuing his risky plan. On the surface, however, Zelenka has worked tirelessly to narrow down the Jumper's probable location, and now has joined Sheppard on a second Jumper for a dangerous rescue mission. He modifies the Jumper's cloak to act as a tenuous shield against the water pressure as Sheppard submerges the vehicle and begins the search. McKay defies Carter's advice — and her creative attempts to distract him — and fires up the drive pods. They activate briefly and then die, proving Carter right and leaving McKay with barely enough power for another half hour. His survival is now up to his friends — and only his hallucination believes they're really on their way, let alone that they can arrive in time.

Sheppard, McKay, Teyla and Ronon visit an oppressed, poverty-stricken village that sacrifices half of every harvest to a mysterious Lord Protector in a great tower — a tower that looks exactly like the central spire of Atlantis. In exchange for the farmers' tribute, the Lord Protector defends them from the Wraith with amazing weaponry. Intrigued, Sheppard's team guesses that the tower, an Ancient relic, must be well-stocked with valuable drone weapons. As McKay sneaks closer to investigate, Otho, the Chamberlain to the Lord Protector, arrives in the village. He scans Sheppard, Teyla, and Ronon with an Ancient device, then forces Sheppard to surrender his gun and pay a visit to the tower. Inside this unsettling copy of Atlantis, Sheppard meets the elderly Lord Protector; his surly son, Tavius; and his attractive daughter, Mara. The Lord Protector quickly grows so weak that he must retire to his chambers to rest. Obviously, one of his children will soon inherit his throne. That evening, Mara aggressively tries to seduce Sheppard. Unnerved, Sheppard seeks answers from Otho, who explains that the royal family carries the Ancient gene that allows them to operate the tower's technology. Despite generations of selective breeding, however, the family's abilities have deteriorated. Recently, when Otho scanned the team, he discovered that Sheppard also possesses the gene. Thus, the Lord Protector promised to designate Mara his successor … if she can revitalize her family's genetic future by marrying Sheppard. Rather than consent to a lifetime of wedded bliss and feudal lordship, Sheppard summons Dr. Beckett. Beckett investigates the Lord Protector's mysterious weakness and offers to treat Otho with his gene-therapy regimen, which allows recipients to operate Ancient technology. Otho is deeply unsettled by the implications of the drug, which could revolutionize the planet's rigid class structure by making "royal" power available to countless peasants. Meanwhile, McKay discovers an entire city — just like Atlantis — buried beneath the tower. He sneaks into its earthquake-prone corridors, hoping to shut down the ZPM that's powering the royal family's advanced technology. At the same time, in the village, Ronon kills a royal constable for abusing a woman; his action inspires the downtrodden peasants to rebel and demand their rights. Back at the tower, the Lord Protector dies just as Beckett concludes that the man was poisoned. The royal court, with an unknown murderer in its midst, plunges into a succession struggle. Worse, the surprise winner then decides to consolidate royal power by making a deadly example of Sheppard, his team, and the entire nearby village.

Above an isolated moon, Sheppard's team discovers two battered life pods in decaying orbits. They bring them to Atlantis, where Dr. McKay opens the first pod. An aged, unconscious woman lies within, near death. When Dr. Weir approaches for a closer look, an energy beam lances out of the pod and strikes her. Weir collapses. She awakens moments later, claiming to be a woman named Phoebus. Because her body is dying, the pod has automatically stored her personality and imprinted it on the first living person to approach. Before Sheppard, Caldwell and the other observers can grow too alarmed by this strange story, Weir seems to resurface. She confirms what Phoebus said and adds that the imprinting will last only a few hours. Before Phoebus's personality vanishes forever, however, she has a request. Her husband, Thalan, is in the second pod. If Sheppard will volunteer to host him, the two can briefly be reunited before they die. Sheppard reluctantly agrees and receives the imprinting. Phoebus greets Thalan with a kiss — but then the two grab whatever weapons are handy and start firing at each other. In fact, they're actually the last surviving opponents in an ancient, devastating war, and each is fanatically determined to defeat the other. As the team scrambles to capture them, Phoebus and Thalan carry their vendetta into the corridors of Atlantis. They have total control over Weir and Sheppard's bodies, can impersonate them perfectly, and also have access to their knowledge of the city. Thalan soon sabotages the power systems, plunging Atlantis into darkness. During the struggle, Phoebus shoots Ronon. The hunt goes on as Beckett struggles to remove the bullet by flashlight. The moment McKay gets the power back on, Phoebus completely locks down the city, trapping everyone in rooms and corridors and blocking all computer usage. Teyla, locked into the same section as Thalan, manages to stun him. Then Phoebus contacts Caldwell — who has assumed command — and threatens to turn the city's fire-suppression gas against its population unless Caldwell helps her defeat Thalan. Knowing that the hazardous gas could kill up to three quarters of Atlantis's residents, Caldwell reluctantly orders Teyla to drag Thalan to a security camera so Phoebus can see her ancient enemy. Pleased, Phoebus then orders Teyla to execute Thalan. But if Teyla fires the last shot in this war, she'll be killing Sheppard, as well.

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.

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.