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Obviously your main goal is to get through each level and kill the final boss, however there are a ton of enemies and mini-bosses between the start of the level and the end boss. In addition to killing the bosses, if you want to get to all of the levels (not to mention see the real end of the game) you will have to get a 98% complete or higher on each level. Your percent complete works just like in Contra Shattered Soldier: every kill gets you a certain percent complete added to your hit percentage and every time you die you lose 1%. How much percent gets added when you kill something depends on what type of enemy it was. Stronger enemies give a higher percentage, while weaker ones only give a single percent. Minibosses, end of level bosses, and individual segments of bosses give percentage points as well, so you must destroy absolutely everything to get a perfect score. After each stage you are given a 'D', 'C', 'B', 'A', or 'S' rank depending on your final hit rate (after you get deducted for deaths and continues). Time and shots fired are not factors in determining your score.

  • S-Rank: > 97%
  • A-Rank: 95%—97%
  • B-Rank: 90%—94%
  • C-Rank: 75%—89%
  • D-Rank: < 75%

In order to advance to stage 5 your average rank must C or better. To advance to stage 6 you'll need a B or better and to get to stage 7 you'll need a ranking of A or S. If your score an S rank after stage 7 you'll get a different ending as well. The goal of Neo Contra is not to simply beat all seven stages (not that hard), but to finish the game with an S rank.

There are also six different weapon sets which greatly affect the difficulty of the game, and three different playable characters.