Alpha

Intelligence program Alpha was the original artificial construct approved for the Special Operations program Freelancer. It was later copied (split into different fragments of emotions) illegally in order to supply multiple agents with an AI.

History
'WARNING! The following section contains MAJOR plot spoilers to Red vs Blue Reconstruction and that of numerous related characters.' Agent Washington has stated that Alpha is/was a "smart" AI, which would make it similar to Cortana. However, since all the AIs from the program were split off of Alpha, it is implied that the AI has all the tactical uses of all the AIs. Personality traits of individual AIs may or may not have been copied from Alpha, as they could either be side-effects of being copied or of rampancy. After several Freelancers attempted to steal Alpha, it was sealed away in an undisclosed location. After Church entered in Caboose's mind and received Delta's message of "Memory is the key", Washington quickly formulated a plan to stop the Meta. He informed the Red and Blues that they were going to Command to steal the Alpha, as its memories were the only thing that could stop the Meta. However, he later revealed to Church that it was the memories of Epsilon that they were seeking.

Washington revealed that all the AIs were created by reverse-engineering a multiple-personality disorder. The Director of Project Freelancer tortured Alpha to the point where it isolated certain aspects of its personality to preserve its sanity. These fractured traits were then harvested and refined into "purified, compartmentalized emotion", creating additional AIs. Washington explained that no AI was a complete personality, that each was an aspect of Alpha that it attempted to preserve or a negative emotion from the result of its treatment. Delta represented Alpha's logic, Omega represented its rage, Gamma its deceit, and Sigma was its creativity. Eventually, the Alpha had to abandon its memories to remain sane, and thus Epsilon was created. In order to keep AIs and Freelancers from finding the AI, Alpha was hidden in a place that no one would think to look; soldier in the middle of nowhere.

Reunion

 * The Alpha AI has come to be known to be just a myth, due to the alarming behavior of AIs actively seeking the AI. As a result it would appear that The Meta's actions are driven by its numerous implants. The AIs seem to have a tendency not unlike the JENOVA Reunion Theory of Final Fantasy VII, in that all fragments of the original entity; no matter how small; have an inherent tendency to reunite with the original. It would appear that the reunion of all the AIs to either complete or restore Alpha is the Metas ultimate goal. This is reinforced by the fact that the Meta seems unable to communicate directly, as is the fact that the sheer amount of AIs that the Meta is using would drive a person insane or even totally obliterate their mind, leaving the AIs themselves to use Maine's body as their medium of interaction with the physical world.

Creation
Copied off the the mind of Dr. Leonard Church the Alpha was split into 8-10 AIs, including Gary, Delta, Epsilon, Theta, Sigma and O'Malley.

Theories
Whether Church really is the Alpha can be disputed due to a number of facts.

For: Against:
 * Washington's observations make perfect sense when looked upon in retrospect; how Church could come back if he isn't a ghost; why he was no different when posessed by Omega; why he always agreed with Delta; and how Omega can take poeple's bodies over.
 * Church turns into a ghost like figure when killed by Sheila, it is stated in episode 17 of the Reconstruction, then why doesn't the soldiers who died turn in to ghosts.*
 * Church is revealed to be the Alpha de facto, and is even projected by Wash's armor before he transfers to Meta to reunite with the other AIs.
 * Tex has also been shown "returning" from the dead and taking over peoples' bodies as well; this would only fit with Wash's belief if she was an AI too.
 * For all we know, she could be. The project could have experimented with givng an AI to another AI; this would also explain why Omega could seemingly control Tex more easily than he could other characters and sought to return to her.
 * Tex's personality seems too well developed to be a mere fragment; both her and Church have loose backstories that most characters don't have. For her to be an AI she would have to be another "smart" AI as well. Unlikely considering the difficulty Project Freelancer would have obtain another one without the UNSC noticing. Though it could be that after the Alpha was tortured the Director had found a way to make another Smart A.I. without needing the UNSC to give them another one.
 * The fact that Church and Tex have intertwined backstory could be explained by the fact that his memories as an A.I. were shed when Epsilon was harvested in order to retain his sanity. His memories of Tex could have been written from scratch in order to keep his identity as Alpha secret.
 * Excellent point. In addition Tex appeared to have been a 'favorite' of the Director for an unknown reason. Maybe, somehow, she was given an additional enhancement: the ability of her AI. She, like Omega and Church (Alpha) was able to turn into a 'ghost' form and 'infect' other people.
 * The epilogue implies that Tex is an AI- however, she was apparently patterned after the mind of the woman that the Director lost in the Human-Covenant War, which simultaneously explains the reason why the Director favored her while also refuting all of the above arguments. Tex's relationship with Church is undoubtedly a reflection with of the Director's own relationship, since Wash said AIs can occasionally inherit the memories of the people they were patterned after.
 * Sarge has a conversation with Church after being shot that is presumably in the "other world", which does not make sense if Church is not a ghost. However, this has never been mentioned again, and could possibly just be a hallucination.
 * Church was possessing Sarge when he was shot, so maybe he was still partially in Sarge's mind.


 * While possessing Donut, Church was seen to be temporarily displaying personality traits of Donut (e.g. offering to braid Caboose's hair), contradicting the theory of him being an AI if he didn't have control over Donut's body.
 * Church was not a 'complete' AI at this point and could possibly have not had full control over Donut and his extremely effeminate character, or perhaps, he was just being silly.
 * It should also be pointed out that Omega also change slightly depending on who he was possessing. For example, when Omega was in Caboose's head, he sounded similar to how he did when he was in Tex.  However, when Omega possessed Doc, his voice changed.  As did the manner in which he spoke.  Perhaps it's part of the nature of the AI's to take on part of their hosts' personalities.

It might be important to note that Church as the Alpha has more or less been confirmed with the final episode of Reconstruction, episode 19.