|Out of universe information|
- "If I remember correctly, you were the one who wanted to — what was it? — run and hide?"
- —Elizabeth Weir
- "I have no friends here, my work is not respected ..."
- —Peter Kavanagh
When Major John Sheppard's team in a Puddle Jumper was stuck in an active Stargate, he was part of the team working on a way to help them. He got into an argument with Dr. Simpson about the possibility of the Jumper exploding and the burning fragments entering Stargate Operations like bombs. She thought it was a very remote possibility, but he thought it wasn't. The other scientists and Dr. Elizabeth Weir sided with her. After Weir told him to "Worry a little bit more about their lives, and less about your own ass," he accused her of humiliating him in front of his team. She threatened to exile him to a barren world alone if he didn't return to work. In the end, however, his idea of blowing up the rear hatch of the Jumper to get forward momentum, helped the ship come through the gate. (ATL: "Thirty-Eight Minutes")
When everybody was asked to record a personal message to send to the 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. (ATL: "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. (ATL: "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. (ATL: "Critical Mass")
Kavanagh later returned two years later as a part of the Midway space station crew, with a shorter hair cut. 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 rescued by the Daedalus. (ATL: "Midway")
- "Kavanagh? What the hell are you doing here?"
- —Rodney McKay
Roughly one year later, Kavanagh was reassigned once again, this time to the Daedalus. While monitoring a sensor, he detected a weak subspace signal that was sent to the Super-hive just before it jumped into hyperspace. Dr. Rodney McKay was able to decipher the signal, revealing that it came from an alternate reality and that it contained the coordinates to Earth. (ATL: "Enemy at the Gate")