Project freelancer was not the only program with an AI. Before that there was a much larger operation, with complete AI. The AI slowly started driving their hosts mad, and at some points even taking partial control away from their host. Then the UNSC decided that the AI's needed to be destroyed. They started taking AI out of humans, but some resisted. They would turn their owner against the UNSC, filling their head with thoughts that weren't really theirs. Then some AI took full control of their host, and began killing guards. Omega was one of those AI, and got tex to leave the area. Then years later, when Project Freelancer freelancer started up, and they were implanting AI fragments, Tex showed up. She had a full AI, hence it being stronger than us fragments.