In an alien city, Mitchell is lying in a room having visions of kissing a woman, then attacking her. He wakes up to find his hands covered in blood and more visions of beating the woman to death and dropping the weapon. There is a pounding on the door, men race in and slam him to the ground, and a man identifies him by name and shows him the dead woman, then places him under arrest.
Twenty-four hours earlier
Mitchell is in a chair with electrodes on his head, and visualizing himself speaking with the soon-to-be dead woman, Dr. Reya Varrick, and telling her about "the ring." He is the ambassador to the outside worlds and gives her a briefing of the things he's seen, and that the project may be their only help for survival. Then Mitchell wakes up and it becomes clear he has a memory from a year ago belonging to the project head, the Emissary. They adopted the memory transfer device from Goa'uld technology, and the planet Galar is currently under the protection of the Asgard.
They return to Earth to brief Landry and discuss the Galaran situation, and that that planet is seeking to build an alliance offering the memory device for Earth's advanced technology. They go back for a gathering and while Daniel worries about the problems with such technology, Mitchell talks with Dr. Varrick until she is called off by another scientist, who hands her a piece of paper. She confronts the Emissary about the fact the military is taking over the project then stalks off. Mitchell goes after her and offers to provide his own influence. The Emissary sees them leave.
They go to Varrick's apartment, the apartment Mitchell saw from the Emissary's memories. They end up in bed together, and the next morning they catch up to the opening sequence. SG-1 is informed by the Emissary that Mitchell is in custody for Varrick's murder and that he's confessed. SG-1 visits him in his cell and Daniel points out it's a memory implant, but Mitchell doesn't feel better because his memories are "real" to him. Mitchell is taken to the Emissary who informs him he is being released to go back to Earth. Mitchell isn't happy even after the Emissary offers to remove/replace the memory. Mitchell insists on a full investigation despite the fact he might be executed.
Landry suspends the negotiations and SG-1 informs him they'll be using the machine to investigate Mitchell's memories with Sam looking on, while Daniel and Teal'c check out the evidence. The scientists checking his memories don't believe Mitchell is guilty and assert the military killed Varrick and framed Mitchell. To establish a baseline, they check into Mitchell's childhood memories of when Mitchell as a child came to the VA hospital where his father was brought to after a test flight accident that cost him his legs. They then jump to a memory of a few months later but realize they'll have to repeat the procedure several times.
Daniel and Teal'c confront the Emissary and note that her personal file has a number of deletions – the Emissary claims the information is deleted for secrecy reasons but has no bearing on the investigation. SG-1 is less than satisfied with his response. The scientists continue to check Mitchell's memories but can find no evidence the memories are false. The scientist in charge, Dr. Marell, reveals that Varrick was his wife (separated for two years) and is obviously convinced of Mitchell's guilt.
Back at SG Command Landry gets a report that Mitchell was stunned by a zat gun and they give the evidence to the Emissary, but he warns it won't be sufficient. They confront Marell, who warns the only way they can confirm the memories are false are by comparing them to similar memories of Mitchell killing an innocent person. They come up with a memory of Mitchell on a flight assignment attacking a vehicle convoy. He gets an abort command just after he drops the missile. Later he is told that the target wasn't in the convoy and he bombed refugees. Marell confirms the memory of the murder was implanted, but Mitchell insists on knowing who did do it.
Next they start looking for anomalies in Mitchell's memories, while Daniel and Teal'c meet with the Emissary. The Emissary is relieved and insistent that he return to Earth, and refuses to allow the scientists to find the real killer due to the distraction from the project. Daniel points out Mitchell doesn't plan to drop the matter and his opinion will be important in the negotiations. Marell and his colleague Amuro initially don't have much luck but manage to find an anomaly and activate it. They go through Mitchell's memories until they get to Mitchell seeing his reflection in a mirror, but the reflection is blurred. They "clean up" the memory and Mitchell can see the face of…Marell.
Marell denies it but Sam suggests Marell killed Varrick and then erased his own memory. Marell agrees to let them test his memories and they find he has the same memory from two different nights – clearly impossible. Marell fooled himself to get rid of the guilt – the perfect alibi. Later Amuro erases the false memories and restore the true ones of him with Varrick. Marell comes in with the Emissary and it becomes clear his memories have been erased and he has no knowledge of the investigation or his memory. After he leaves, the Emissary reveals they've altered Marell's memories so he believes Varrick died in an accident, and that now he can continue for the good of the project.
Back at SGC, Landry commiserates with Mitchell over the bombing incident and reassures him that he's glad Mitchell didn't resign over it. Mitchell remembers back to his dad, learning to get by on new artificial legs, and how he convinced him not to give up his career over it.