Ah yeah, I did forget the "quasi-soul." That makes things potentially easier.
Alpha never really does anything outside his prime directive until after the defeat of Omega-M/F. He certainly went above and beyond the scope for which he was intended, but until then he just got us to fight Omega's test subjects and then Omega itself, which is the entire reason he was created. Going on a journey was the first independent thing he willed himself to do outside of his intended purpose.
Might be why we can't Echo-talk with mammets - they have some degree of intelligence, but no real will of their own. Except maybe Vivi.