I ran a game with two players back in the late '80s, so it was 3rd ed. There really wasn't much that is different than running a larger game. You might scale back the encounters a little so that they are not overwhelmed. My 2 player group did make a really bad choice and TPK'd. That is a risk you will run.
If your player survives to make contact with some non-hostiles, you can always add some friendly NPCs like locals or rescued MP personnel to let them have a try at some larger targets. In combat, you will basically just be like the last two sentences of the first paragraph on page 85 under INITIATIVE.
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