After their temporary alliance with the Wraith backfires, the Atlantis team must find a way to stop two Wraith hive ships that are headed for Earth. Weir orders Colonel Caldwell to attack the Hive ships using the Daedalus and the Orion before she is ordered to return to Earth to account for her team’s failures. Sheppard , who was able to survive by latching his F-302 to the hull of a Wraith ship, is forced to rely on a now ostracized Michael to help him save McKay and Ronon , who are being held prisoner by the Wraith. Ronon and McKay are able to free themselves from their cocoon prisons with a plan to sabotage the ship in a last act of heroism. All plans collide as the Daedalus and Orion engage the Hive ships while Sheppard, McKay and Ronon are still aboard.

Having successfully used the Wraith retrovirus to turn an entire hive ship of Wraith into humans, the team returns to Atlantis with their prisoners in stasis. Weir continues to defend her leadership in the face of an independent review being conducted by IOA member Richard Woolsey . Examining the hive ship that the team hijacked in an attempt to restore it to full working condition, McKay discovers that the Wraith prisoners cannot continue to be held in stasis indefinitely. The team decides the best thing to do is to set them free on a planet under the guise that they were exposed to a viral outbreak. Sheppard and Dr. Beckett remain on the planet to manage the human-form Wraith, including a re-humanized Michael. But when they discover a Wraith ship approaching the planet, the team must act fast to keep the existence of Atlantis a secret.

While looking for suitable stargates to harvest for their new Intergalactic Bridge, the team comes across a small village with a revered leader. To their surprise the village’s leader, Lucius , has an obnoxious manner and an utter lack of credibility. On Lucious’ request, Weir sends Dr. Beckett to determine if any of Lucious’ potions are worthy of trade. Though at first put off by Lucius, Beckett soon becomes so enamored by his host he disobeys security protocol and brings him to Atlantis. By the time Sheppard and McKay return from another stargate harvesting mission, they find the entire base has fallen for Lucius’ unctuous charm. Believing foul play is at work, McKay discovers that Lucius is using some sort of pheromone to enchant those around him. It becomes clear that unless Sheppard can remove the now entrenched and protected Lucius from Atlantis, there will be no stopping his charming coup d’etat.

Exploring a village, the team is suddenly attacked and taken prisoner. It turns out that Ronon had visited the planet before, and unknowingly lured the Wraith there. The Wraith then made a pact with the villagers that if they capture Ronon and contact them, the village will be spared from any future culling. On Ronon’s request, the villagers set Sheppard and Teyla free, who then quickly mobilize a strike force to return to the planet and save Ronon. Upon their return, however, the team finds the village devastated and Ronon taken. Back in the hands of the Wraith, Ronon is again implanted with a homing beacon and set free on his devastated home planet of Sateda, to once again be hunted by the Wraith. Ronon recalls the fall of his homeworld, where his wife and comrades were killed by the Wraith years ago. After the team determines Ronon has been taken to Sateda, they must race to the planet to save him.

Scouring the Atlantian database Dr. Rodney McKay discovers a reference to an abandoned Ancient testing site. Investigating the site, the team discovers a vast metropolis supporting millions of Ancients. Eager to create an alliance with such an advanced society, Weir is shocked when their leader Oberoth refuses the offer.
Seeing no way to appeal to their humanity to help save the Pegasus galaxy from the Wraith, Weir and the team head back to Atlantis. However before they are able to leave, the team is ambushed and taken prisoner by Oberoth and his guards. The team is then subjected to a mind probe by what they now discover are actually replicators in the form of Ancients. Having created the replicators as a weapon against the Wraith, the Ancients feared they were losing control of their creation. But the Ancients’ attempts to destroy the replicators failed. Now, the surviving replicators are divided – some wish to mimic their creators and seek ascension. Others, including Oberoth, want nothing more than the destruction of Atlantis as revenge for the Ancients’ betrayal. Now the team must find a way to free themselves and stop the replicators from reaching Atlantis.

Waking up in a psychiatric hospital outside of Washington D.C., Dr. Elizabeth Weir is shocked to discover that her entire experience in Atlantis over the last two years was solely a figment of her imagination. Through the help of her psychiatrist Dr. Fletcher she learns that a car accident that killed her fiancé left her in a near catatonic state and suffering from delusional psychosis. Forced to come to terms with this new reality Weir is visited by her mother and General Jack O’Neill , who assures her that he has never heard of a Stargate program let alone the lost city of Atlantis. Yet as she starts to pick up the pieces of her life she continues to have unsettling visions warning her that she must return to Atlantis. Back on Atlantis the team holds vigil for the comatose Weir, who in reality has been infected by replicator nanites that are quickly taking over her body and mind. Even with the medical expertise of Dr. Carson Beckett and the emotional support of Lt. Colonel John Sheppard , it is ultimately up to Dr. Weir to save herself and find a way back to the real world.

Summoned to a planet by a communication code they had previously given their Genii allies, the team is ambushed by Kolya who has now created his own faction of Genii after being forced from the inner circle of the Genii leadership. While the rest of the team manages to escape, Sheppard is taken prisoner. Unable to track down Sheppard on their own, the team reluctantly contacts the Genii's new leader, Ladon Radim. But they have no way of knowing if Ladon is involved in the kidnapping. When Kolya finally contacts Atlantis, however, he offers to free Sheppard, but only if the Atlantis team turns over Ladon, who Kolya intends to drain Sheppard's life by allowing a captured wraith to feed on him. Sheppard's life is slowly drained in successive video taped feeding sessions, while Weir struggles with the decision of whether or not to meet Kolya's demands. Meanwhile, Sheppard forms a bond with his cellmate, who is also a prisoner of Kolya. With a rescue unlikely, and his time running out, Sheppard forms an unlikely alliance to attempt an escape.

Rodney McKay is called back to earth to convince his estranged sister, Jeannie Miller, to assist the Air Force in implementing an important mathematical proof that has application to one of McKay's experiements. Having not seen her in four years, McKay finds it difficult to pry Jeannie away from her family, so he has no choice but to disclose the existence of the Stargate program to her.McKay and Jeannie travel to Atlantis, and begin the experiment, which is intended to generate limitless energy by bridging parallel universes. The experiment is initially successful, until a Rodney McKay from the parallel universe appears in the experiment's containment chamber asking the team to shut down the experiment to avoid damaging his universe. And this Rodney MKay, preferring to be called "Rod", is the polar opposite of our McKay, with charisma, courage, and humility in spades. Rod forms an instant bond with Jeannie and the other members of the Atlantis team, causing McKay to become instantly jealous. While at first believing the crisis to be averted, the team soon realizes that shutting down the experiment from their end won't prevent ROd's universe from being destroyed. And what's worse, people in Rod's universe have a plan to save their own universe at the expense of ours. Now Jeannie, McKay and Rod must find a way to save both universes, and may have to make certain sacrifices in the process.

Major Leonard’s team fails to check in with Atlantis while on a mission exploring an anomalous energy spike. Because the anomaly also makes radio transmission impossible Sheppard must assemble a team in search of the missing men. When the team arrives on the planet they’re shocked to find the bodies of several Genii soldiers who have apparently killed each other. Following the energy readings in hope of finding Major Leonard and his men Rodney McKay leads the team into a cave to discover that the cause the anomalous energy spike is some sort of Wraith generator. Rodney’s investigation of the device is cut short when Teyla finds the all the missing team’s dead bodies except for Major Leonard who it appears to have killed them all. Realizing something isn’t right and in need of reinforcements the team takes the deceased back to the gate only to be ambushed by Major Leonard who has rigged the gate’s DHD to explode taking out three marines.Trapped on the planet and with no way to send radio transmissions the team falls back to the cave in a hope to deactivate the wraith device. While McKay struggles to shut down the device and Carson Beckett attempts treat the critically wounded marines, Ronon takes off chasing what he believes are wraith in the forest. With Sheppard and Teyla in hot pursuit things quickly turn ugly as Ronon turns his fire on them and Sheppard is forced to return fire in defense. Before they realize it both are succumbing to hallucinations believing the other is the enemy.

While testing the new McKay-Carter intergalactic gate bridge, the Daedalus detects an Ancient Atlantian warship, traveling at just below light speed and heading towards Earth. Damaged in battle during the war with the Wraith, the Ancients aboard this ship fled the Pegasus galaxy and have spent thousands of years in stasis. Back on Atlantis, the now awoken Ancients meet with General O'Neill and Richard Woolsy .They thank the Stargate team for taking care of the city in their absence, but ask them to vacate Atlantis immediately. While Ronon and Teyla stay in the Pegasus galaxy, the remaining team members struggle to resume their lives on Earth. Sheppard doesn't gel with his new SG team, McKay is bored in his Area 51 lab, and Weir has trouble finding meaning in a life after Atlantis. However, the SGC soon learns that the Replicators have overtaken Atlantis, as McKay had previously enabled the Replicators to re-write their own base code to override a safeguard preventing them from killing the Ancients that made them. Now, with O'Neill and Woosley trapped in Atlantis and Gernal Landry intent on protecting Earth by sending nuclear weapons through the gate to destroy Atlantis, the team must figure out a way to save O'Neill, Woolsey and Atlantis itself.

Teyla begins to see apparitions of ancients in distress and believes they are the ghosts of the Ancients recently massacred by the Replicators. Meanwhile Rodney McKay believes he’s found the whale that saved him a year ago while trapped in a submerged puddle jumper. But while taking a jumper out with Col. John Sheppard to investigate his old friend they discover the whale is not alone but is one of dozens of its kind, all headed directly to Atlantis. With their high pitched sonar the whales begin to painfully affect the inhabitants of Atlantis. Teyla, whose visions are now being shared by others, believes it’s this threat the whales pose that the ancients are trying to warn them about.

Sheppard and his team hear of a great warrior with stories of defeating both the Genii and the wraith and decide to seek him out in hopes of making a powerful new ally. But when they learn this great warrior is none other than Lucius they believe he’s up to his old tricks again. Testing him for his enamor-inducing herb they find he’s clean and only really guilty of pawning off their battle stories as his own. Claiming he is in fact now invincible his demonstration of his power reveals he’s actually found one of the Ancient’s personal shields. Ready to leave him about his ways the team is ambushed by angry raiders and must rely on the invincible Lucius to be save them. Sheppard not willing to believe all is as it seems follows Lucius to learn he is actually in cohorts with the raiders; really a disgraced band of Genii personal guards. Deciding to blow the whistle on Lucius’ scam the danger suddenly becomes all too real when Kolya shows up demanding the Atlantis team be handed over to him. With Lucius used as bait the whole team except Sheppard is taken prisoner. With no way of reaching Atlantis for re-enforcement it’s up to Sheppard to save the team before Kolya begins his promised executions.

Trying to preserve power by turning off all the non-essential systems the Ancients recently activated before being killed by the replicators, Rodney McKay mistakenly is hit by an energy beam from a mysterious device. His worst fears are quickly laid to rest when Dr. Beckett gives him a clean bill of health and returns him to active duty. Not long after the incident Rodney begins to display advanced powers such as amplified senses and telekinesis. Unable to ignore his powers Rodney and Zelenka discover the machine that zapped him actually accelerated his evolution. Basking in his new found super power, exponentially growing intelligence and equally bloated ego the team struggles to deal with the new Rodney. But envy turns to concern when Weir uncovers the true nature of the ancient device. Designed to accelerate a person’s evolution it was designed to speed up the process of ascension. However without being able to achieve the same advancement in mental state the machine killed most the ancients that ever tried to use it. Death looming as he continues to physically evolve Rodney tries to crack the secret of ascension in quantified terms. With no success in site he resolves to use his final days making peace with his colleagues and friends even if they aren’t ready to give up on him just yet.

Major Lorne discovers a planet with dozens of satellites in geosynchronous orbit. However, inhabitants on this plante are no further advanced than being themselves in a renaissance period and even stranger, he discovers a flag baring Rodney McKay’s likeness. Informing Rodney and Lt. Col. Sheppard of this, the team realize a game they had found years earlier on Atlantis might actually be much more than just a game. Realizing that an ancient sociological simulation actually sent orders to two competing city-states, Weir demands that McKay and Sheppard set things between the once peaceful neighbors right. Meeting each of the cities representatives, Nola and Baden the two men find that their dipolatic mission may be much more difficult than they thought. Before they have time to usher in a new peace, the two cities take matters into their own hands and embark on a world war with much more advanced weapons than the Atlantis team were aware of. The two bickering friends must find a way to stop it or be responsible for what could be the destruction of two civilizations.

With the entire city ordered to take a personal day the team does their best to unwind and enjoy their leisure time. Without warning a mysterious explosion rips through the city killing and injuring unsuspecting citizens. Dr. Rodney McKay and Dr. Carson Beckett arrive on the scene to find Teyla critically injured by shrapnel from the explosion. Unable to find explosive residue, the only leads they have to go on are eyewitness accounts saying one of the base-scientists just suddenly exploded. McKay, realizing the scientist in question is one of his own, quickly puts the pieces together to learn that the incident is likely the cause of an Ancient device mistakenly activated days earlier by two of his scientists. The device which is actually a type of weapon infects nearby organisms with a tumor-like explosive that detonate after reaching critical mass. Knowing that the other scientist is still somewhere on the base the race is on to track down the man who is literally a walking time bomb before he explodes and injures more people

Deep underwater, the team scours the ocean floor looking for a mobile geothermal drilling station the ancients left dormant in hopes of unleashing near limitless power from beneath the planet’s surface. The team finds the drilling rig and cautiously explores the station the Ancients chose to abandon. Using her gift Teyla thinks she senses the presence of a Wraith but repeated life scans by McKay (David Hewlett) show nothing out of the ordinary. Weir , believing it’s just the pressure affecting Teyla, has the team press on to explore the station. Without warning, Teyla suddenly attacks Ronon and sets up a series of force fields to block the team from the jumper. But when Col. Sheppard (Joe Flanigan) corners her she has no memory of doing anything wrong. Using Teyla successfully as a puppet a Wraith Queen, now aboard the station, attacks two scientists to lure Sheppard to the jumper in hopes of using him to fly her to the surface. Unable to overcome the power of the Queen, Sheppard is helpless and saved only by Ronon mistakenly blasting the jumper windows sending a wall of ocean water onto Sheppard and the Queen. With the Wraith Queen now restrained and sedated Teyla uses her gift to learn that the Queen was part of the first wave of attacks on Atlantis. Her cruiser was shot down sending it plummeting to the ocean depths. Surviving only by feeding on her crew, she woke between centuries in the hope of a rescue that never came. Sensing Teyla’s presence as they descended she awoke knowing the ship she sought had finally come. Wanting to either escape her watery prison or die the queen activates a self-destruct on her ship. If the team is unable to stop the resulting explosion over the thin layer of crust the drilling station sits on it would ignite a catastrophic chain reaction.

After helping relocate the Taranans, the Atlantis team realizes they haven’t heard from the village in an unusually long period of time. Wondering what happened to them, Weir sends Sheppard and his team to go investigate their village. Once there, it appears the Taranans have just abandoned their village until Rodney McKay detects life signs well beneath the surface in the remnants of the previous village’s underground industrial complex. Searching the dark winding corridors of the abandoned tunnels the team comes upon some sort of cocoon as well as a lab that appears to have been used for Wraith experiments. Discovering the bodies of several Taranans who appeared to have been fed on by the Iratus bug, the team has little time to piece the puzzle together before they themselves are attacked by a large insect-like monster. Their weapons are useless against the creature’s exoskeleton. Ronon is barely able to fend it off by cutting off one of its arms. Radioing for backup, the support team manages to make it through the gate just moments before a wraith dart scoops them up. Back in the tunnels Teyla becomes separated from the team and taken prisoner by the scientist who created the beasts, Michael . He explains that after being treated as an outcast by his own people, unable to live as a wraith or a human, he decided to create an army of his own. Using what he learned from Dr. Beckett’s retro-virus and through experiments of his own he’s been able to build a super bug. Having used the entire Taranan village as food for his experiments, he plans to use Teyla to the same end.

With the arrival of the Apollo to Atlantis comes intel that the Replicators appear to be building a large armada to directly attack earth. Planning to strike first, Col. Ellis with the aid of the Atlantis team launches a surgical strike nuking the entire armada. Believing that all imminent danger has been avoided the team is shocked when a satellite housing a stargate takes up geosynchronous orbit above Atlantis. Unable to destroy the Stargate, it opens transmitting a powerful energy beam impacting Atlantis’ shields. Being powered from the point of origin, neither the beam nor the satellite’s shields show any vulnerability to the Apollo or Atlantis. Without any way of avoiding the beam as it quickly drains the ZPM powering the shields, Rodney McKay opts to sink the city as the ancients did millennia ago using the water to dissipate the beams strength. But when the sinking of the city doesn’t have the desired effects, it appears it’s only a matter of time before the shields fail. With the stargate active in such close proximity, it renders the city’s gate inactive. Their only hope is to use what energy the ZPM has left along with strategic cover by an asteroid to hopefully fly the city into hyperspace before the shields collapse. But when the asteroid fails to hold, allowing the beam to cut through to the city, it seems unlikely Atlantis will make it off the surface in one piece.