I think there's just a 'finite' number of enemies, but a few trucks will arrive when you try to get into the sub.
To get into it:
Take the welding-thing next to one of hatches, take your man off the welding-thing, remark your unit and now a welding-icon will appear over the hatch. After a few more minutes your unit will get into the sub automatically. Then take one of your man to the generator to open the sub-pen (press "o" and klick on the binoculars if u don't knwo where to go) and the mission is finished.
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