- "With the Wraith in disarray, Michael returned to the human populations he'd infected with the Hoffan drug. He selected the strongest and the healthiest of the survivors and converted them to hybrids. The rest he exterminated."
- —Rodney McKay
After Lt. Colonel John Sheppard was transported 48,000 years into the future and Teyla Emmagan had her baby, Michael Kenmore was able to speed up the distribution of the Hoffan drug to Human planets and create more of his Hybrids. With the International Oversight Advisory and the military reluctant to commit a lot of resources to protecting the human populations of the Pegasus galaxy, Colonel Samantha Carter was forced to take action. Finally, they decided to give her a new ship – the Phoenix barely off the assembly line. After placing Major Evan Lorne in temporary command of Atlantis, she and her team spent the better part of a month getting it ready for combat. Once the ship was fully functional, she flew the ship in an attempt to destroy Michael's fleet. (ATL: "The Last Man")
- "They were able to inflict considerable damage, despite terrible odds."
- —Rodney McKay
They started a series of hit-and-run ops on Michael Kenmore's fleet, destroying several Hive ships with their Asgard plasma beam weapons and escaping back into hyperspace. This worked for a while, until Michael deliberately leaked some intel that he was about to attack a heavily populated human world. Colonel Samantha Carter thought she could get there first, but she was wrong. The Phoenix emerged from hyperspace only to fly directly into an ambush of 3 of Michael's Hive ships.
Taking intense fire from the Hive ships, the Phoenix took evasive actions, but it was a futile effort. With the Asgard plasma beam weapons down, they fired several Nuclear warhead, damaging the Hives, but not destroying them. When the Phoenix's hyperdrive overloaded, Carter beamed the entire crew down to the planet below. However, after the crew was safely off the ship, she lost the transport system. With her engines about to go critical, she figured she didn't have anything to lose. She rammed the Phoenix into one of Michael's Hive ships, resulting in a powerful explosion which destroyed the remaining two. (ATL: "The Last Man")
After the Phoenix was destroyed resulting in Colonel Samantha Carter's death, the Atlantis expedition was forced to stop helping human populations altogether and Richard Woolsey took command of the city. Appalled by the thought of sitting around and doing nothing while innocent humans were left to die, Dr. Jennifer Keller and Dr. Rodney McKay left Atlantis via the Daedalus and returned to Earth, McKay only to return several years later to restore the timeline to how it should have been. The battle was prevented after the future was changed when Michael Kenmore was defeated and his cruiser was destroyed by the Daedalus after Teyla Emmagan was rescued. It was prevented forever when Michael was killed by Teyla when she threw him from the top of Atlantis' Control Tower. (ATL: "The Last Man", "Search and Rescue", "The Prodigal")