wow, you're still on #2? It gets harder.
There is no trick to it. Just follow your commander's instructions. In fact, you're not even supposed to be in Neptune until otherwise asked to go there. If you go there before you are told you, then you're making yourself a target.
As for the fighters showing up, well, uhm, just take them out? Even if time runs out, as long as you survive, there are no penalties other your not getting any medals, EPs etc.