Gamma

Intelligence Program Gamma, also known as Gary, is an artificial construct, based on Deceit, created for the Special Operation's program Freelancer. It's assigned agent was Freelancer Wyoming.

Implantation
Implanted into Freelancer agent Reginald (Wyoming). Following The Epsilon incident, Gamma forcefully removed himself from Wyoming, causing him mental harm. Gamma and Omega were also used against the Alpha in tests that the Alpha would purposely fail, driving it mad.

The Time Loop
Somehow Gamma found himself inside a computer terminal 1000 years in the past, most likely using Wyoming's time control device. There, he met up with Church and claimed to be the guardian of The Great Weapon. He told Church that The Great Destroyer (who at the time was believed to be Caboose, and then Tex) would destroy the facility and everyone in it in 1856 years.

In order to prevent this, Church ordered Gary to construct a teleportation device to take him to Blood Gulch to prevent Caboose from reaching the base, as well as preventing other unfortunate events. To pass the time during the 1000 years of construction, Gary told Church knock-knock jokes.

After failing miserably at his mission, Church joins up with the Red and Blue Team members and orders Gary to shut off the bomb, Andy, whom he does not get along with.

Siding With Wyoming
Gary saves Wyoming from Tex after the events of Out of Mind, by teleporting him to the housing facility. When Wyoming ambushes the Blue Team, Gary takes over the tank that used to house Sheila, and when Wyoming is sniped by Church, Gary creates a time loop, creating hundreds of Wyoming clones but somehow Tucker caught up with the time loop and he used that to destroy most (if not all) of the Wyoming's and escape from Gary.

Gary is later trapped by Sheila behind a firewall of Sister’s transport ship.

Reconstruction
Gary is mentioned during the replay of Sheila's flight logs, implying that Sheila's firewall keeping Gamma failed. This would allow Gamma to escape, but later Gamma was captured by The Meta.

Gamma was presumably destroyed by the EMP.

It's possible and, judging by Epsilon-Delta's comment, highly likely that the memory of Gamma lives on in Epsilon.

Revelation
Gary is mentioned by Tex in Standardized Testing. Tex reveals that the Freelancer base was where Alpha was sent after the very first break in, which Tex herself led, and it was here more and more "tests" were run on him. Other AI were used in the torturing process of Alpha, with Omega and Gamma being used to create tests that Alpha would purposefully fail, driving him mad, and breaking him to the point he could not recognize anybody, not even Tex. When Church asks if she and the other Freelancers succeeded, Tex says no, and that she failed herself and Alpha.

Kills
Gamma managed to kill Caboose when he was in the tank but Wyoming used his special ability so Caboose only died in an alternate reality, multiple times.

Other

 * When the Alpha AI was split into the other AIs, Gary was it's deceit, explaining his deception of the Red and Blue Teams.
 * Voiced by Mac OS X voice synthesizer, system voice "Fred"
 * According to York, after Wyoming's implantation with Gamma, he had a tendency for telling terrible knock knock jokes.
 * Like O'Malley, Gary's common name may be a portmanteau of his official name (Gamma) and Wyoming's real name (Reginald).