Alpha

Intelligence program Alpha was the original artificial construct approved for the Special Operations program Freelancer. It was either copied or broken down in order to supply multiple agents with an AI. It is unknown -and unlikely- that Alpha was ever assigned to an agent.

History
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 copied from 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.

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 Meta's ultimate goal.