remember aquanox and auanox2 as roughly set at the same time. so in aquanox2 when you help freeman get to the jumpship in optional mission, flint has put the word out. hence you come face to face with three sub's, who's leader even advise you they want freeman and to return his sub back to flint.
it you liston to the chat, it explains why they are there to stop freeman from getting on the jumpship.