- "I have no friends here, my work is not respected..."
- ―Peter Kavanagh[src]
When everybody was asked to record a personal message to send to their loved ones on Earth, he instead choose to record one to Brigadier General Jack O'Neill, detailing everything he thought Dr. Elizabeth Weir had done wrong since their arrival. While Ford started off recording for him, he quickly grew annoyed and left Kavanagh to do his "whining" by himself. (SGA: "Letters from Pegasus")
In a discussion over whether to stay and fight, he believed that 200 people, mostly "scientists who’ve never even fired a gun before", were no match for tens of thousands of Wraith without the Atlantis' shield or primary defenses. Dr. Rodney McKay was surprised to find himself agreeing with Kavanagh. (SGA: "The Gift")
He left Atlantis after the siege. He returned a few months later but requested to leave again just three weeks after that because he didn't feel welcome. He was aboard the Daedalus en route to Earth when the message of an agent of The Trust having infiltrated Atlantis arrived. He was their prime suspect in sabotaging the city, but he was found innocent. He was threatened by Ronon Dex to give up the code needed to save the base (the one he didn't know), but he fainted before Ronon even touched him. (SGA: "Critical Mass")
Kavanagh returned two years later as a part of the Midway space station crew, with a shorter haircut. During the invasion of Midway, the Wraith held him hostage (once again, he promptly fainted in fear). He caused and survived the destruction of the Midway Station, escaping in a Puddle Jumper escape pod with the others and being rescued by the Daedalus. (SGA: "Midway")