SG-1 finds a world desolated by war, with apparently no remaining survivors. They investigate a device in a small complex set apart from the city, which appears to be more technologically advanced. The device may be a weapon of some sort; the Pentagon will certainly be interested.
Jack O'Neill and Teal'c go exploring while Daniel Jackson attempts to decipher an inscription outside. But inside the structure, Samantha Carter is struck by a powerful form of energy while studying the device. She is knocked unconscious.
Back at the S.G.C., Dr. Janet Fraiser declares her healthy -- but is cautious, considering everything Sam has been through over the last four years, and tells her to take some time off. Sam insists on helping SG-16 with the alien device, but General Hammond and O'Neill order her to go home and relax.
The next morning, Sam has a brief encounter with a man outside her home. Moments later, she finds him inside, wanting to talk with her. He claims to be an alien from 636, who followed her back through the Stargate. Sam doesn't know what to make of the stranger, and runs.
She calls in a sweeper team from the S.G.C., which finds nothing. Cameras and listening devices are placed throughout her home, but the alien does not show himself for days. Though her friends believe she is losing her mind, Sam insists that he is real. When the devices are removed, he returns.
The alien -- Orlin -- convinces Sam to let him finish what he started on the planet Velona. He believes that a human can handle the "sharing of souls," if she is prepared for it. She cautiously agrees, and the process is complete; Orlin shares his true essence with her. In so doing, he falls in love with her.
Orlin is a member of an ancient race that long ago ascended from physical form to a spiritual form. Carter believes his race is the same as Oma Desala's, the alien being who raised Shifu, the Harcesis child ("Maternal Instinct"). They both take the same ethereal form, and have the ability to control the weather.
Carter does not tell her superiors that the alien has returned; Orlin threatens to simply disappear again. But she continues her reluctant relationship with him, trying to gather information. In so doing, she learns the terrible truth about the planet Velona.
Orlin tells her that Velona was under attack by the Goa'uld, and that he showed the people there how to construct the highly-advanced weapon to defend themselves -- a violation of one of his people's highest laws. But after the Goa'uld were repelled, the people began to plan the conquest of other worlds. The others of Orlin's kind came and wiped them out to "correct" Orlin's mistake -- sentencing him to live alone on the desolated planet.
Carter cannot convince General Hammond and the Pentagon (represented by Colonel Frank Simmons) to stop the weapons test. SG-16 has integrated a naquadah reactor, thanks to Sam's help, and prepares to activate the weapon. And when she learns that the Pentagon has been spying on her and Orlin, Sam is confronted by Simmons.
The Pentagon calls in a strike force to surround Carter's home and capture him. But Sam has grown close to Orlin over the last few weeks, this alien who has taken human form and forsaken his ethereal nature and powers for her -- and has started to like him. She goes inside ahead of the team, and finds Orlin busy in the basement.
He may have given up his alien abilities, but he certainly still has the knowledge that goes with it. Orlin has constructed a miniature, single-use Stargate to take him back to Velona. He activates the gate, and Sam follows him through as the strike team rushes into the house.
On Velona, Orlin throws himself in front of Colonel Reynold's gun to stop the test fire of the weapon -- knowing that if it is activated, the others of his kind will return, and humankind may suffer the same fate as the people of Velona. Orlin manages to disconnect the power source, and the ignition sequence is terminated. He is near death.
But the others have returned, he tells Sam, and have given him a second chance. They help him to ascend once again to an ethereal form, and he destroys the weapon and leaves.