Major Sheppard finds Dr. Weir alone outside on a landing getting some fresh air. He surprises her with a birthday present which he had made by the Athosians on the mainland. Although she is curious, Sheppard won't say how he found out when her birthday was. He leaves to continue the exploration of the vast huge city complex.
During a room to room check with Teyla and Lt. Ford, they come upon a laboratory. As they are checking it out they find the body of an old woman in a glass chamber. After assembling more people to investigate, they determine the old woman is still alive, but barely, and in a metabolic stasis. The system readout says she has been in stasis for 10,000 years. Dr. McKay insists they revive her immediately, as she may not have much longer to live. Dr. Beckett is more cautious, saying that to revive her might kill her. Weir orders the old woman be revived.
Once the old woman awakens and starts talking, it is clear she knows things about the SGA team that no one else could. That's when the old woman tells them she is Dr. Weir too! Unfortunately the Old Weir keeps falling asleep before she can give them any more information. They also don't know the meaning of a note with five gate address they found on Old Weir. In a meeting to discuss how Old Weir might have traveled to the past, in order to reappear in the present, they speculate on the possibilities of time travel. McKay says it's possible but improbable.
Finally, Old Weir wakes up long enough to begin telling them the story of how she got there. She tells of her team's initial arrival to Atlantis, and how the city began to power up on its own, but that the control panels didn't power up. McKay interrupts her to say things didn't happen like that at the first arrival. Old Weir corrects him, saying she is talking about the first time her team first arrived. Everyone looks around puzzled at this, but before they get an explanation, Old Weir falls asleep again.
Later Weir confers with Beckett on ways to keep Old Weir awake long enough to get the answers they need. Beckett is hesitant to give Old Weir stimulants for fear it will kill her. Weir convinces him that Old Weir would want it.
After a period of time, when Old Weir is more alert, Weir takes her in a wheelchair on a tour of Atlantis, and then to a meeting with the others. Here Old Weir continues the story of her team's first arrival to Atlantis. She says when they came through the gate, the lights came on, but the control panels did not. Once the other McKay had interfaced with the Ancient computers he noticed the power levels were dropping very rapidly. So rapidly the energy shield protecting the submerged city from the ocean water was beginning to fail. The city was starting to flood. Old Weir called for everyone to fall back to the gate room, but it was too late. Many of the soldiers securing the perimeter were trapped by the raising water, and the raising water was headed toward the control room!
Old Weir, remembering one of the team members said there were space ships in a bay, sends the other Sheppard to check them out for possible evacuation use. When the other Sheppard finds one Puddle Jumper is different from the rest, Old Weir goes to check it out too. As they are checking out this Puddle Jumper, the control room gets cut off from the Jumper bay by bulkhead doors. The control room begins to flood, blocking any possible exit by the Stargate. The other McKay tries to open the Jumper bay doors, just as he perishes.
Weir interrupts and asks Old Weir why the city's fail safe didn't activate and rise the city to the surface? Old Weir explains there was no failsafe in place for her team's first arrival.
Old Weir goes on, saying that she, Sheppard, and Dr. Zelenka are stuck aboard the odd Puddle Jumper in the flooding Jumper bay, when Sheppard suddenly activates the Jumper's controls. As he touches another control, they instantly appear in orbit over the planet. Just as quickly as they appear in orbit, they find themselves being fired on by other ships. They don't know what's going on or what to do. However, before she could go on, Old Weir loses consciousness.
Upon reawakening she continues her story, saying one minute ships were shooting at them in space, and the next she was waking up in Atlantis. She awakened to find an Ancient named Janus close by. Janus explained to her that her ship crashed and was found at the bottom of the ocean, and that she was the only survivor. Janus also tells her the ship she was in was a time travel ship that he himself had built.
Once Old Weir is feeling better in old Atlantis, she is taken before the Lantian council. The council welcomes her, but then tells her about their terrible conflict with the Wraith and their imminent evacuation to Earth. Old Weir asks to be allowed to return to her own time to try to save the Atlantis team when they arrive, maybe even take along a spare ZPM, but the council refuses due the problems with time causalities.
Although the council refuses to help Old Weir, Janus agrees to. He sets about calculating the power requirement need to keep the city dormant for 10,000 years and still have enough power left to support the arrival of the Atlantis team. In order to have enough power, the three ZPMs powering the city will need to be switched from running in parallel to running the three, one at a time. However, to do this he tells her, someone must stay behind to switch between the ZPMs as each one is depleted. Old Weir agrees to stay behind and switch the ZPMs as needed.
As the Lantians evacuate to Earth, Janus tells the council that Old Weir was in one of the first groups to go, and so they didn't realize she was still hiding in the city. Janus then programs a stasis chamber for Old Weir and in case she does not survive the 10,000 years, he also programs a fail safe to make the city rise to the surface if power levels reach a critical low point. Janus then departs Atlantis with the final group of Lantians, leaving Old Weir to complete her task.
As Old Weir finishes her story to Weir, she asks if McKay has figured out the meaning of the paper with the five gate address they found on her. She tells Weir that each gate address corresponds to an Ancient outpost, and each outpost has a ZPM. As Weir excitedly goes to tell the news to McKay and Sheppard, who are asleep nearby, Old Weir quietly passes away; her job done.