Remember Aquanox and Aquanox 2 are set roughly at the same time. So in Aquanox 2 when you help Freeman get to the jumpship in an optional mission, Flint has put the word out. Hence, you come face-to-face with three subs, whose leader even advises you they want Freeman and to return his sub back to Flint.
If you listen to the chat, it explains why they are there to stop Freeman from getting on the jumpship.
