Although Dr. Weir has told no one that today is her birthday, Maj. John Sheppard has found out. He gives her a gift: a ceramic jar made by one of the Athosians. Then he, Lt. Ford and Teyla go off to explore more uncharted areas of Atlantis.
The trio finds a lab with an Ancient stasis chamber. Incredibly, the chamber contains what appears to be a still-living, very old female Ancient. Later, Dr. Carson Beckett estimates the woman's physical age to be roughly 100 years. Technically, according to Dr. Rodney McKay, the woman is in a state of metabolic stasis - aging slowly but not entirely suspended. McKay calculates, based on the initial data he was able to access, that the woman has been in the stasis chamber for 10,000 years. Beckett worries that reviving her in her fragile state will kill her. Weir gives the order: Revive her.
In the infirmary, Weir is stunned when the woman, emancipated from the stasis chamber, awakens and recognizes her, McKay, and the entire Atlantis team. Her next utterance is even more confounding: She says she is Dr. Elizabeth Weir.
The elder Weir explains that she found a way to travel back in time, to when the Ancients lived in Atlantis. She has waited more than ten millennia in that stasis chamber for Team Atlantis to arrive.
When the elder Weir is strong enough, she tells everyone how relieved she is to see the city back on the ocean surface. It didn't rise when she and Team Atlantis first arrived in her timeline, because the city had no fail-safe. In her original timeline, Team Atlantis' arrival seriously drained the city's energy reserves and the shield collapsed. Water crashed in, flooding every room in the city. Everyone drowned except Sheppard, Weir and Zelenka; the trio escaped in a modified puddle jumper. Sheppard's Ancient gene had allowed him to activate the ship; suddenly, they were in space, with many Wraith vessels firing at them. The next thing the elder Weir remembers is awakening back in Atlantis ... 10,000 years in the past.
Janus, an Ancient scientist, told her that the Ancients had retrieved the jumper from the ocean floor, and that she had been the only survivor of its crash. The ship was a time machine of Janus' design. He brought her before the Council, which was busy preparing to evacuate the city's occupants to Earth through the stargate. The Council, fearful of further time-tampering, denied Weir's request to return to her own time with a ZPM to prevent the shield from collapsing.
Despite the Council's ruling, Janus devised a plan: He showed Weir the three ZPMs that simultaneously power the city. Used in sequence, they could sustain the power needed to maintain the shield for the time required. The catch: someone had to remain behind to rotate the power from one to the other over thousands of years. To that end, Janus programmed the stasis chamber to awaken Weir periodically during her 10,000-year slumber. He also entered the commands to commence her final revival at the moment that the city's sensors indicated the presence of Team Atlantis, and he programmed a fail-safe system that would raise the city to the surface if power levels dropped below a critical threshold. Then he and the other Alantians evacuated, leaving Weir alone to do her job - a job well-done, as it turned out.
The younger Weir is sad that her older counterpart gave up her life. But the elder Weir feels that her adventure is just beginning, through her younger self. She tells Weir that the five stargate addresses on the note she had in her hand are to outposts - each one with a zero-point module: a gift from Janus. Then she passes away.
Dr. Weir puts the ashes of her older self in the ceramic jar that Sheppard gave to her, then scatters them over the city. Her older self has given her the ultimate birthday present: a future.