Oh nice! I have a feeling that Corporal Adrian Shepard is on the boat some how, probably also in stasis. One would assume the portal gun or one just like it is on the ship which needs to be taken and used to better serve humanity against the Combine.



However in my head, GLaDOS has somehow also did a time dilation or something where her test subjects, both Resistance and Combine are stuck in perpetual hell as they have to keep redoing the tests/obstacle courses and reliving their deaths over and over again. Only saving GlaDOS from the trap itself does she allow you access to the portal gun on one condition however. The Resistance is allowed to leave the ship, but the Combine must stay their trapped forever to conduct more tests/experiments.



Either that or as you said GLaDOS made her own army of walking tanks like Terminators, but with them being a little more... odd in behavior, but no less deadly.