You start in a long corridor with three powerups, a Weapon, a Shield, and a Flame, at the other end. Grab what you want and head right... to face every major boss in the game, again. *shudder* Luckily, they are all the same as before. Every time you get a game over, you'll start in the corridor again, and you can fight the same boss you lost your last life on.
The first six bosses should go down quickly since you know what to do and have more experience now. You can't do the Gravity Jump trick against the stage 5 boss here but the stage 6 boss should be easier now because you have access to a readily available Weapon powerup. After you defeat all six major bosses again, you can move on to the final boss of the game.
Previous bosses
A large white machine will slowly move from the right to the left side of the screen, gradually exposing the four cores in it's center. Jump up and destroy them as the machine moves along but you have to be quick since you're on a strict 30 second time limit. After all four cores are gone, it will blow up and the game will end. Congrats!