The game has 4 different endings:
ENDING 1: Easy-Mode Mockery
If playing the game on Easy mode, the game will end after completing Stage 5. After defeating Robot X, you see an unresolved ending with Mr X that hints at playing the next difficulty mode.
ENDING 2: The Unresolved
If you fail to save the general/chief, you'll branch to play Round 7B (The City Hall/The White House). At the end of this, you have to face a stronger Shiva as the last boss, instead of Robot Y (known as Neo X in Bare Knuckle 3).
ENDING 3: The Disaster
If you do rescue the general/chief, you'll branch to play Round 7A (The Robot Facility). You are expected to defeat Robot Y within a time limit. If you beat it after the timer expires, the bombs will still detonate in the city, turning it into a complete ruin.
ENDING 4: The Best (Canon)
Same as ENDING 3, but destroy Robot Y before the timer expires. The bombs are defused and the city is saved. This is the best (and Canon) ending of the game.