The private notes of the SGC's CMO
On their return Colonel O'Neill and Major Carter were both physically and mentally evaluated. The stress of being marooned off world was well documented to produce severe reactions in the finest of officers. They were separately debriefed at length and both wound up in cells. O'Neill was deemed the most dangerous and least likely to follow orders remained confined. Major Carter's condition was taken in consideration and was released. They weren't allowed to communicate with each other. While Colonel O'Neill understood that there was extreme pressure on General Hammond and this was his only option, he appeared resentful and thoroughly angry at the situation. Major Carter felt her freedom betrayed her loyalty to O'Neill. They were both given the out of "alien influence – get out of jail free" card to explain their current state. They independently refused and allowed the process of a court martial to begin. I do not think this will affect Colonel O'Neill, except perhaps for his blood pressure, but am somewhat apprehensive about its effects on Major Carter.
Excerpts from the Court Martial of Major Samantha Carter
Prosecution: "Dr. Lee, did you ever witness Major Carter acting in an inappropriate manner in regard toward Colonel O'Neill?"
Dr. Lee: "Sir I have known both of these officers for many years and…"
Prosecution: "Would you please answer the question." The officer demanded.
Dr. Lee: "It was a very long time ago and it was under duress."
Prosecution: "Doctor Lee"
Dr. Lee: "When Colonel O'Neill was lost through a transportation device of Furling design, Major Carter became extremely angry when my team of technicians packed up to go back to Earth."
Prosecution: "Why were you leaving?"
Dr. Lee: "We could not make any head way. The technology as completely foreign to us and I deemed it a waste of our time. The project was useless."
Prosecution: "Why did Major Carter object then?"
Dr. Lee: "Because Colonel O'Neill was lost and this was the device that caused his disappearance."
Prosecution: "Was she emotional?"
O'Neill was uncomfortable with this incessant line of questioning and had the ardent desire to punch out the JAG officer but instead sat tall and stared straight ahead.
Dr. Lee: "She was extremely angry. I think she felt somewhat to blame for what had happened. She, herself, had been working non stop for the week we were there and she was probably very tired."
Prosecution: "No further questions."
The defense rose.
Defense: "Dr. Lee, when were Colonel O'Neill and Colonel Maybourne found?"
Dr. Lee: "About 4 weeks later."
Defense: "What was their condition?"
Prosecution: "I object; Dr. Lee is not a medical doctor."
Judge: "Over ruled"
Dr. Lee: "Colonel Maybourne was never returned to the SGC but I heard that he had been shot twice, quit seriously."
Defense: "And Colonel O'Neill?"
Dr. Lee: "Colonel O'Neill, I believed spent over a week in the infirmary with shrapnel wounds to his leg, from a grenade. I also heard that they were both poisoned by a plant, which we were given to study. It was psychotropic causing delusions and paranoia."
Defense: "Would these men have fared betted if they had been found earlier?"
Dr. Lee: "Of course"
Defense: "Who figured out where Colonel O'Neill was?"
Dr. Lee: "Colonel O'Neill's team, SG-1"
Defense: "Headed by?"
Dr. Lee: "Major Carter."
Defense: "Not emotionally running off in a myriad of directions but steadfastly approaching the problem with clearheaded logical thinking."
Dr. Lee: "Yes sir."
Defense: "No further questions of this witness."