During the Battle of M2S-445, Michael Kenmore escaped his cruiser via a commandeered Puddle Jumper moments before it was destroyed by the Daedalus. However, the Atlantis expedition thought he died along with his ship, unaware of his escape. (SGA: "Search and Rescue")
After Michael's defeat, he still needed Teyla Emmagan's son Torren to finish perfecting his Hybrids. However, the only way to do this was to infiltrate Atlantis. So, Michael modified his captured Puddle Jumper, giving him an advantage over the unsuspecting Atlantis expedition. (SGA: "The Prodigal")
Michael Kenmore invaded Atlantis using the Puddle Jumper and an IDC stolen from Major Nelson, bringing several Hybrids with him. Having converted the cloak into a stun field, Michael stunned everyone in the Control Room and shielded himself from further invasion from the outside. He disabled the city's power, running Stargate Operations solely off the Jumper's power source, and locked out the transporters to the Control Room and Gate Room.
Michael's goal in doing all of this was to kidnap Teyla Emmagan's son Torren and destroy Atlantis via the self-destruct in order to kill everyone inside for revenge for what the Atlantis expedition did to him. Even though he had Teyla and her baby, he refused to leave until he had set the self-destruct, which was taking awhile due to it being highly encrypted.
Dr. Radek Zelenka managed to get minimal power up and due to closed circuit security cameras, everyone became aware of who invaded the city. Because of the stun field, no one was able to get to the Control Room to stop Michael, and Major Evan Lorne was stunned in an attempt. In a room where all of the people stunned initially were kept, Ronon Dex and Technician Amelia Banks regained consciousness, and Amelia managed to get the door open and to defeat the Hybrids guarding it. Ronon, two Marines, and Richard Woolsey headed to the control room to try to stop Michael and his forces. The two marines were stunned, but Ronon fought Michael, allowing Teyla to get away. Ronon lost the fight and gets thrown off the Control Room balcony, knocking him out and giving him a concussion.
Teyla and Woolsey (who she hooks up with) ran away from a Hybrid, but Woolsey was knocked out by the stun field during the escape. Teyla managed to defeat the hybrid by knocking him into the stun field, and hid in the entrance to the power conduits. Michael then activated the self-destruct to draw her out, promising to deactivate it and leave Atlantis intact if she comes with him, but when Teyla told him to deactivate the self-destruct to prove it. He refused and started to leave, planning to use Torren's DNA to clone him and continue his research that way.
He went to kill Ronon, but before he could, a plan that Dr. Rodney McKay and Lt. Colonel John Sheppard came up with was set into motion: McKay flew a Puddle Jumper out of the Underwater Jumper bay and dialed the Gate after Zelenka remotely lowered the Stargate shield. The unstable vortex destroyed most of Michael's Puddle Jumper, killing the Hybrids inside it and cutting power, disabling the stun field and self-destruct. Michael's remaining Hybrids were killed by a strike team led by Sheppard and Michael himself was wounded by Sheppard. Michael attempted to steal another Puddle Jumper to escape, but Zelenka closed the Bay roof, trapping him. Chased by Sheppard, Michael climbed out onto a balcony at the top of Atlantis control tower where he and Sheppard fought in hand to hand combat. Sheppard was losing until Teyla showed up and knocked Michael off the balcony, leaving him barely hanging on. Teyla kicked Michael's hands off the ledge, sending him falling hundreds if not thousands of feet, killing him. (SGA: "The Prodigal")