The Phoenix Campaign refers to a series of battles that occurred in 2383 throughout the Pegasus galaxy in an alternate timeline. This campaign was part of an effort set forth by the Atlantis Expedition to push back against the forces of Michael Kenmore and his assault against the human populations of Pegasus galaxy planets.
In 2383 in the present timeline, Lieutenant Colonel John Sheppard stepped through the Stargate on M4S-587 with the intent of returning to Starbase Atlantis. However, the Stargate's wormhole was intersected by a solar flare, which transported him 48,000 years into the future. With his absence from the present, a timeline emerged in which Teyla Emmagan had her baby while a captive of Michael Kenmore. As a result, Michael was able use the baby's DNA to complete his research into perfecting his Human-Wraith Hybrids. Furthermore, he was able to speed up the distribution of the Hoffan drug to Human planets throughout the galaxy.
The Pegasus galaxy descended into chaos - humans and Wraith alike were under attack by Michael and his growing army of hybrids. With the International Oversight Advisory and the leaders on Earth reluctant to commit any significant resources to protecting the human populations of the Pegasus galaxy, Colonel Samantha Carter was forced to take action.
As a result of persistent lobbying, the IOA finally yielded in their position, deciding to assign Earth's newest BC-304, the Phoenix, to the Atlantis Expedition for use in repelling Michael's crusade. As the ship itself was still incomplete upon arriving at M35-117, Samantha Carter and Dr. Rodney McKay spent the better part of a month getting it ready for combat. Once the ship was fully functional, Carter herself commanded the ship, leaving Major Evan Lorne in temporary command of Starbase Atlantis in her absence.
The campaign began as a series of hit-and-run ops against Michael Kenmore's fleet; the Phoenix would emerge from warp, inflict as much damage as possible on the enemy using quantum phasers, and escape back into warp before incurring any significant damage. In one such engagement, the Phoenix emerged from warp facing two of Michael's Hive ships. Taking both by surprise, the Phoenix was able to completely destroy one of the ships with only a handful of shots. However, before the second one could be destroyed, it opened fire on the Phoenix, which promptly withdrew as to avoid taking damage.
Initially, the Phoenix campaign showed great promise in repelling Michael's forces. Determining this one ship to be a serious threat, however, Michael Kenmore staged an ambush. He deliberately leaking intel that he was about to attack a heavily populated human world. Colonel Samantha Carter, believing the intel to be correct, thought she could get to the planet first and prevent the attack. However, upon emerging from warp at the coordinates, the Phoenix was immediately ambushed by three of Michael's Hive ships.
The Phoenix's last stand
The Hive ships immediately targeted the Phoenix. Taking evasive action, the Phoenix attempted to return fire. However the intensity and persistence of the Hive ships' weapons began draining the Phoenix's shields and caused damage to several systems, including the quantum phasers. Unable to utilize them for defense, the ship's entire complement of torpedoes were fired in response. The ensuing barrage of torpedoes raced towards the two nearest Hive ships, causing substantial damage to their outer hulls upon impacting but failing to completely destroy them.
Within minutes of the engagement, as a result of extensive battle damage, the Phoenix's warp drive began to overloaded. Unable to reroute the power to another system, Samantha Carter beamed the entire crew down to the planet below. However, the transport system went offline moments later. With no way off the ship and the engines about to go critical, she figured she didn't have anything to lose. As her last act, Carter rammed the Phoenix into one of Michael's Hive ships. The resulting explosion completely destroyed the Hive ship and the Phoenix, and produced a shock wave powerful enough to completely destroy the remaining two Hives.
After the Phoenix was destroyed, the Atlantis Expedition was placed under the command of Richard P. Woolsey. Furthermore, the IOA instituted a new policy in which all expedition personnel were recalled to Starbase Atlantis from their present assignments elsewhere in the galaxy to instead focus solely on the starbase's defense. This mandate effectively cut the Atlantis Expedition off from the humans of the galaxy who desperately depended upon them for both military and medical defense against Michael and the Hoffan drug. As a result, Michael now had free-reign over the galaxy and was able to proceed with his crusade largely unopposed.
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 Starbase Atlantis via the Daedalus and returned to Earth. McKay would return to Starbase Atlantis several years later to put in place measures to restore the timeline to how it should have been. These measures ultimately allowed John Sheppard to return to the present timeline. As a result, Teyla was located before she could have her baby. This prevented Michael from perfecting his hybrids, and the entire Phoenix campaign was prevented. Michael Kenmore's cruiser was destroyed by the Daedalus over M2S-445, severely crippling his crusade. In one last effort to revive it, he would later launch an assault against Starbase Atlantis, ultimately resulting in his death at Teyla's hands.