This Puddle Jumper was one of three rescue ships sent to M2S-445 after a booby-trap collapsed Michael's facility there upon the Atlantis expedition members within. After rescuing Doctor Rodney McKay and Major Evan Lorne, the rescue team was forced to retreat into orbit in their cloaked Puddle Jumpers after Michael's cruiser appeared in orbit and blocked the Stargate so that they couldn't escape. Eventually, the Daedalus arrived and after taking out the cruiser's hyperdrive, lowered its shields briefly so that the crew could beam aboard Lt. Colonel John Sheppard and Ronon Dex. While the Daedalus shields were lowered, the three Puddle Jumpers landed aboard.
During the battle that followed, the Daedalus launched F-302s to take out the cruiser's main weapons and the First Atlantis Reconnaissance Team took this Puddle Jumper to board the cruiser when it launched Wraith Darts to counter the fighter attack from the Daedalus. Despite a narrow opening, the Puddle Jumper was able to safely make it aboard the cruiser and the team left it parked under cloak while they went to rescue Teyla Emmagan. After they blew up the cruiser's hyperdrive, Michael realized that they had gotten onboard somehow, located the Puddle Jumper and stole it to escape with a few of his Hybrids. Discovering the Puddle Jumper gone, the team and Kanaan were forced to steal a Wraith Dart to escape. The cruiser was destroyed soon after by the Daedalus and Michael was believed to be killed in the explosion. (SGA: "Search and Rescue", "The Prodigal")
A few weeks later, when discussing Michael's potential survival with Richard Woolsey, McKay reminded Woolsey of the missing Puddle Jumper and suggested, correctly, that Michael stole it to escape. Despite Michael requiring the ATA gene to use Ancient technology, McKay theorized Michael might've created a gene therapy of his own that allowed him to fly the Puddle Jumper. (SGA: "The Seed")
Eventually, Michael was able to modify the Puddle Jumper to emit a "stun bubble" by interfacing Wraith stun technology with the Puddle Jumper's cloaking device and used it as a Trojan Horse to invade Atlantis. During the invasion, Michael parked the Puddle Jumper on the Gate Room floor and used it as an external power source to power the Control Room and "stun bubble." At the end of the invasion, Doctor Radek Zelenka remotely dropped the Stargate shield, enabling McKay to use another Puddle Jumper to dial the Stargate to a random planet and use the unstable vortex to vaporize the rear third of the Puddle Jumper. Any Hybrids inside the rear compartment were vaporized as well and power was cut to the city, ending the "stun bubble" and the activated self-destruct, enabling Sheppard to lead a strike force that defeated Michael and his Hybrids. (SGA: "The Prodigal")
It is unknown what happened to the remains of the Puddle Jumper following the death of Michael and the end of his crusade.