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Neo Contra has several different endings, which one you get is determined by your average ranking and the end of stages 4, 5, 6, and 7.

Part I: The Contra Commanders[edit]

These stages are available in both easy and normal modes and can be completed in any order. Your mission in each stage is to assassinate the Contra Commanders, one at a time. All that stands in your way is the entire Neo Contra army. Along the way you'll meet a rather odd ally as well as an old friend of Bill.

Part II: Red Falcon[edit]

In order for stage 5 to be unlocked, you must have an overall ranking of C or higer in normal mode. It wouldn't really be a Contra game without Red Falcon, would it? He's back (sort of) and is in need of some good old fasion killing.

Part III: Project C[edit]

You will automatically move from stage 5 to stage 6 if you overall ranking is B or higher. Likewise, you will only move to stage 7 if your overall ranking is A or S. Having disposed of the rest of Neo Contra, it is time to take out the leader, Master Contra. Kill him and the truth will reveal it's self - just not in the way Bill was expecting.