A team of scientists think they have found the location of the long lost city of Atlantis. It can be reached by a Stargate address that leads to the Pegasus galaxy.

A strange energy generating fog allows travel back to Earth. But something's wrong.

While Teyla and Ronon investigate the mysterious death of Major Lorne, the Genii Ladon Radim contacts Atlantis. He wants to trade a ZPM for weapons supplies.

The hive ship approaching Atlantis is Michael's. He wants a trade: the retrovirus for not revealing the secret of Atlantis and insights on Wraith technology.

John Sheppard is kidnapped by the Genii and is in the company of a Wraith.

With everyone having a Sunday off - something recommended by psychologist Dr. Heightmeyer - all of the members of the Atlantis team pursue leisure activities. Rodney McKay and Carson Beckett are scheduled to go fishing; Sheppard decides to teach Ronon Dex about golf; Teyla spends some time in the gym; and Elizabeth Weir has a lunch date with the handsome Mike Branton. Their day off however is interrupted by a powerful explosion near the mess hall killing and injuring several members of the team. McKay thinks he knows the cause of the problem - a device found by two junior members of his team may have turned some of them into walking time bombs by creating explosive tumors in them.

Having been told by the Genii spy on New Athos that her people were still alive, Teyla asks permission to visit a man named Davos who is a legendary seer and may be able to help her. When they arrive, Dr. Keller realizes that the man is dying. His ability to see the future is real, but the snippets of the future he is able to show them are open to interpretation. John is called back to Atlantis when they receive a message from the Wraith whose life he had previously saved. He offers to work with McKay to fix the nano virus that is now malfunctioning. As if this weren't enough happening, Richard Woolsey arrives from Earth to undertake Samantha Carter's 3 month evaluation.

Keller, Carter and McKay are stranded in an abandoned Genii mine while off-world.

After yet another fruitless search for the missing Teyla, Sheppard returns to Atlantis, only to find it deserted. Worse yet, the city isn't just abnormally hot, but the entire ocean has completely dried up, leaving a sandy desert! Sheppard then finds a hologram of an aged Dr. McKay, telling him that a solar flare had sent him 48,000 years into the future. Once he learns the demise of Atlantis and everyone on it, and worse yet that the sun in the solar system is dying and he won't survive there much longer, he and the holographic McKay must find a way to send Sheppard home and potentially change all of this.

Dr. Carson Beckett is removed from stasis because he's the only one who can find the antidote to a mysterious virus that has incapacitated base personnel, beginning with Dr. Jennifer Keller.

A group of beings stranded in sub-space seek help from Atlantis to return to normal space. But their outrageous claims and erratic behavior strains the trust of their benefactors and forces a painful solution.