Tex has been a source of confusion for the fanbase numerous times. First, there was the song "A Girl Named Tex" which said her real name was Beth, not Allison, and gave her a completely different backstory from what would be established later. There's also the scene from Season 1 where Tucker says her black armor indicates she was in the special forces at some point, even though she never was. Lastly, her flashback in Out of Mind makes no sense knowing that both Church and Tex are AI. I realize that all three of these examples are just because they didn't know what direction the story would eventually take, but Red vs. Blue has found plenty of ways to explain weird things from the Blood Gulch Chronicles before, so I figure there must be an explanation for all of this too.
In The Prequels, we found out that Church's original body was that of a human, and it first belonged to none other than Private Jimmy. This calls something to question: Where did they get Tex's body from? She must've had a human body, since she knew nothing about her true nature until C.T. filled her in. Well, despite the Director and Allison being married, Church and Tex only remember dating in the past, and Private Jimmy sure talked a lot about his "girl back home." Maybe she wasn't actually at home and that's just how Jimmy refers to her. Maybe she was Tex's host body.
Now let's talk about the song. Jimmy's girlfriend is never given a name, so let's suppose that it's Beth and the song is partly about her. The first lyrics of the song are
"Have you heard the story of a girl named Beth, now known as Tex"
In other words, she used to be Beth, but now she isn't. Then the song explains that Beth always wanted to join the military, but her father didn't approve of it because she's a girl. The song says her main motivation was money, but it could've also been because she wanted to "help her fellow man." Maybe her somewhat-selfless reasons for volunteering inspired Jimmy to join the military too. Beth was good enough to get into the special forces, while Jimmy wasn't quite cut out to be a soldier and just ended up as a mere simulation trooper.
After several successful missions, Beth catches Project Freelancer's attention. The Director decides that her skill and her similarities to Allison would make her the perfect host body for the Beta AI. Not knowing what was really going to happen to her, Beth decides to join. They give her a black suit of armor to reflect her previous position in the special forces. Jimmy tries to warn her that Project Freelancer is suspicious by telling her about the rumors that they're sticking computer programs in people's heads, but she dismisses it. However, Jimmy would be proven right once she was sacrificed to give Allison a human body. Post-implantation, Tex remembers that conversation as if she had it with Church. I know Private Jimmy was in that flashback, but considering Church remembered him as a separate person, it's not impossible that Tex would too.
Much, much later, the people at Project Freelancer need to hide the Alpha and find him a body. Even though there was only a slim chance of memory contamination from the host body, they wanted to find someone who had a past relationship with Beth, just to make absolutely sure there's no inconsistent memories that will lead the Alpha to question things. Luckily, her boyfriend happened to be working under Project Freelancer as a simulation trooper. Captain Flowers is sent to find him, and the events we see in Why They're Here happen from there.
And that's my theory. What do you think?