She Sells Alien Cells By The Seashore (Or: Ray Plays Contra: Hard Corps)*
Due to the open ended nature of the game, here's the layout:
Intro Level
*decision: 2 possible second levels*
Junkyard (Contains hidden ending)
Rainforest (May or may not contain a certain cutscene depending on which level 2 you completed)
*decision 4 Possible Ending levels, depending on which decision you made here and at the end of level 1*
The Junkyard boss fight, the jungle level, and the decision path for the best and good ending (if you decided to rescue the research center after level 1). These levels are common across both possible routes through the game.
This branch occurs if you decide to keep going. It'll take you to the best ending, as well as the "complete bastard" ending. It's one of the harder paths to take, IMO.
Level 2 alternate, and a rerun/revenge attempt on motherfucking Noiman Cascade.
If you pursue deadeye joe, this level set happens in lieu of the research center level. It's somewhat harder but considerably more badass. Sadly, all of the endings that happen on this route are a total kick to the nuts.
After this level, you get dumped to the junkyard level, and then you have to do the jungle level. Which is completely the same except the boss is slightly different (and harder) and the cutscene with deadeye joe doesn't happen. Everything looks completely the same up until the final level.
This occurs if you both pursued joe and chose to keep fighting. This ending is by far the hardest to get as far as I'm concerned, and it is so not fucking worth it. I cannot overstate how much I loathe this ending. Even if a classic contra boss drops by to say hi.