With the Wraith ships headed for Earth, Sheppard must find a way to rescue Ronon and McKay. Meanwhile, the IOA makes life hard for Dr. Weir.

As the Hive ship arrives above Atlantis, everyone is happy to find that Col. Sheppard and team are in control. However, the Wraith crew, now turned back in to humans using Dr. Becket, 's gas, must be dealt with in some way. Michael, who now has separately been reverted back to his human form, and the reverted Wraith crew, are relocated to an unpopulated planet which lacks even a stargate. Dr. Beckett then refuses to leave the planet until he is sure the former Wraith won, 't revert back to their former state, as Col. Sheppard and team plan to leave back for Atlantis.

At the same time, IOA Agent Richard Woolsey travels back to Atlantis with Dr. Weir to evaluate her command there.
Things do not go as planned, and Dr. Beckett's life becomes endangered. Sheppard and his team must take the crippled Hive ship back to try to rescue him, as a second Wraith ship approaches the planet Dr. Beckett was left on.

As Shepparda 's team searches for unused gates to build an easier and faster path back to the Milky Way, they happen on a simple agrarian culture on a planet with an unused orbital gate. There the find Lucius, a town folk who seems to be extremely loved by all those around him. When Dr. Beckett later brings Lucius back to Atlantis unannounced, things there become strange too. Lucius seems to be able to control everyone in Atlantis, except for Col. Sheppard, who has had a recent cold. Sheppard must find a way to overcome Luciusa ' control over the crew, before he becomes a target for opposing their new guest.

Ronon and the team visit a friendly planet, only to find it unfriendly to Ronon, as Ronon brought the wrath of the Wraith down upon them, when they took Ronon in years before while he was a runner. The villagers plan to send them to the Wraith as a sacrifice, as the Wraith has promised not to cull them if they do. Ronon is finally able to get the villagers to at least send his friends back to Atlantis. The team later returns with reinforcements, but Ronon is gone and the village destroyed. Meanwhile, Ronon has been re-implanted with a Wraith tracking device and dropped on the ruins of his home world a Sateda,a with the Wraith chasing him again as a Runner. Ronon also begins to experience flashbacks to his past on Sateda, and to the earlier Wraith attacks there. Even as the Atlantis team searches for him, Ronon has plans of his own, and a goal he has set to attain for himself, before he can be allowed to be killed by his trackers.

Atlantis discovers one of the Ancientsa ' abandoned research outposts, that turns out not to be abandoned. However, they find they have found a Replicator community living in an even greater a Atlantis like city, part of which also has the capable of space flight. The learn the Replicators have always wanted to emulate the Ancients, and have also wanted to exceed them. However, they want, but cana 't duplicate the Ancientsa ' final step of ascending. Now the Atlantis team must escape these Replicators, but not before they also extract the knowledge they have to defeat the Wraith.

Dr. Weir awakens in a psychiatric hospital only to be told her memories of the last two years of her life were false; just a figment of a psychotic episode she has had over the last two days, after collapsing after a treaty negotiation. Even a visit by Gen. Oa 'Neill to tell her that Stargate Command and an off world Atlantis doesna 't really exist, doesna 't convince her. Then, strange events and changes she sees at the hospital cause her even more doubt about if what is going on around her is really real. Can she discover the truth of her situation, and can the people she thinks are real back in Atlantis; rescue her from this seeming nightmare?

In a convoluted plot to regain power over the Genii, former Commander Kolya captures Col. Sheppard, in order to bargain for the capture of the Genii Ladon. Strangely, Sheppard is able to find an ally in the person being used to scare Atlantis into turning over Ladon, that being the Wraith Kolya is allowing to feed on Sheppard every three hours, a Wraith.

In a strange twist, McKaya 's sister, an accomplished scientist and now a a stay at homea mother, may have found the solution to creating new ZPMs with out knowing it. But McKaya ' sister, Jeannie, is reluctant to either assist the military, or help out her brother, whom she has not heard from for over four years. However, once onboard, McKay and Jeannie put her theoretical physics formulae into practice. The problem is the process that will give them a new power source will also produce a dangerous exotic particles.a Jeanniea 's theorem could allow for these dangerous exotic particles to be sent instead to a parallel universe; one that the odds are will be uninhabited, hence not endangering this universe. During the start up test phase, they are surprised to receive the a McKaya from the parallel universe they are targeting. He tells them that the exotic particles being generated, are about to destroy his universe. The team must find a way to fix this error, which could also endanger their own universe. At the same time, McKay must also put up with the nicer parallel version of himself, and also try to repair the tension that has existed between him and his sister.

When Sheppard leads a team to find another overdue off-world team, they find the team members are all dead, except for their C.O., who is still missing. Theya 've all been shot numerous times with their own weapons. They also find the decaying remains of several Genii soldiers, who have also died violent deaths, some months before. When Shepparda 's team try to return to Atlantis with their dead, they find the DHD has been rigged to explode, which leaves them stranded on this dangerous planet. It appears that an unusual device they have found, which is emitting strange EM pulses, may be the cause of the hallucinations they are all starting to have. However, can they fight off these hallucinations which were the cause of their comradesa ' deaths, long enough for McKay to figure out how to turn off the mysterious device?

While Atlantis and Earth successfully test a a multiple gatea bridge between their two galaxies, the Daedalus detects another ship. When they try to make contact with the ship, the ship drops out of its time dilated hyper-warp. They learn it is a Lantian war ship returning from a long journey, headed back to Atlantis. When the Lantian crew learns that all their people had all left Atlantis ten thousand years ago, and that they are the only ones that remain, they politely ask the SGA crew evacuate back to Earth. Gen. Oa 'Neill and Richard Woolsey arrive in Atlantis to try to negotiate with the Lantians, but they are reluctantly forced to agree to leave Atlantis, while Ronon and Teyla decide to stay behind in the Pegasus galaxy. However, the newly found Latians turn out to be overly confident on their ability to control an impending attack by the Asuran Replicators. Gen. Oa 'Neill and Woolsey then become trapped on Atlantis; as Sheppard, Weir and the rest of SGA break rank with the SGC to try to rescue them and defeat the Replicatorsa ' attack on Atlantis. Dr. McKay can get them back into the heart of Atlantis, but what sort of resistance will they encounter?

Sheppard and his team, along with Weir and Beckett, arrive in the Asuran's city and destroy the Replicators' stargate operations. The team then escapes, and tries to reprogram a Replicator that had been left floating in space, in order to freeze all the Replicators, so they can rescue O'Neill and Woolsey. However, after O'Neill and Woolsey are captured, the team must come up with a plan B. as plan A has failed. The team goes about this new plan and feeds Woolsey misinformation, as they suspect he will be probed by the Replicators. But will this new plan succeed where their original one failed? Time is against them.

When McKay finds his a whalea circling the floating city, strange events begin to occur. Teyla begins to see people that arena 't there. Then Weir begins to see the same people too. Soon everyone begins to see visions of Ancients who appear to be in distress. Can the arrival of McKaya 's whale be connected to these visions? Can the visions the team are seeing forebode an impending event? Also, can the team make sense of the weird voices they are hearing during their visions, in order to understand the unknown danger in front of them? McKaya 's answer leads to a daring plan by Sheppard that might just possibly save all the biological life on the planet.

Sheppard and his team head to a planet to investigate reports of a superhero in hopes this person might help in their struggle with the Wraith. What they find is a person they have had to unfortunately deal with in the past. However, soon after this meeting, an even worse foe turns up when word spreads that Sheppard is on the planet.

While trying to find ways to conserve power in Atlantis, Rodney stumbles upon a room that is using large amounts of power. In an attempt to shut it down he gets hit with a beam and starts developing super powers.

Major Lorne investigates a planet where one civilization has pictures of McKay, and SGA soon realizes it is connected to an Atlantis control room that McKay and Sheppard had found and thought was just a game room. SGA soon realizes the game room was really an experimental Ancient control room which controls the planet. McKay and Sheppard find that their war game has been affecting the real people on the planet for the last few years. Now Sheppard and McKay must convince both sides that their planeta 's struggle was a mistake that they both mistakenly caused. However, they soon learn that they may have led these people into all out war with the technology they mistakenly provided.

Shepparda 's team discovers a space station filled with humans locked in a transporter module for hundreds of years. They bring two of them out of status, Jamus and Herick, and are told the survivors 'froze themselves in the hopes of outliving the Wraith who were attacking them. However, an explosion causes the station to fall out of orbit and traps the team throughout the base.

It's a typical Sunday in Atlantis and everyone is going about their daily lives. A handsome scientist, Dr. Branton, who is smitten with Dr. Weir is trying to convince her to go to lunch with him. Although Dr. Weir has a personal rule against dating the people under her command, he persuades her to just have lunch with him.

During lunch, Dr. Branton kisses Dr. Weir and she becomes attracted to him, but she decides she can't allow anything to come of this; then the control tower reports that there was an explosion and three people are dead and many injured, and it is believed to have been a bomb.

While exploring an ancient drilling platform that could provide Atlantis with more power, the team gets cut off from the jumper and there might be a Wraith after them.

When Atlantis loses contact with people on Taranis, Weir sends Sheppard and team to investigate. At first they find no life signs, but as they investigate further it appears there is at least one life sign deep underground. Their investigation soon leads them to an old foea 's horrific research which could soon alter the balance of power balance in the galaxy, leaving all humans in an even greater peril than from even the Wraith.

A failed attack on a Replicator armada forces McKay to follow in the footsteps of the Ancients, millenia before, and take a drastic step to save Atlantis from destruction.