Your character is seen running in place at an inhumanely fast pace against a sky backdrop. The camera pans out to show that you are running around the top of a helicopter.
You will immediately be attacked by twelve green wasps which must be destroyed with lock on weapons (12%). They usually come in sets of three and fly around for a few seconds before attacking. Once they are out of the way you will be attacked by another Helicopter. Hit it as quickly as possible with lock on weapons, stopping only to clear out the mines when it becomes to dense. It takes a lot of hits, but can be destroyed with patience (17%).
- Several missiles come flying at your helicopter, and one of them destroys the helicopter that was just attacking you. All of the missiles miss, but then a battle cruiser appears near you and opens fire.
The Battle Cruiser itself cannot be destroyed, instead you must take out eighteen different guns with lock on weapons (35%). The Cruiser isn't very hard, but you don't have much time to destroy the guns before the helicopter changes positions and the targets are out of range.
- A huge battleship flies in and pushes the cruiser out of the way. It opens fire on your helicopter, destroying it, but not before Bill and Jaguar jump aboard the battleship.
Things can get ugly in this section since there are a lot of ninja-grunts, mortar cannons, and very narrow spaces. When you first get aboard, take out the two armored soldiers (37%) and then the stationary helicopter (38%). Move forward and kill the two snipers (40%) and then the helicopter than gets lifted up by a crane (41%). Head back down and to the right to destroy the helicopter and turret (43%) and then the helicopter and turret to the left (45%). After they are taken care of head back up and kill the two armored soldiers across from where the crane was (47%).
Now you have to deal with four bazooka soldiers, two snipers, two armored soldiers, and two turrets (57%) around the corner. Right past there are two hover crafts (59%), two docked helicopters (61%) and a turret on a narrow walkway (62%). To destroy the turret wait until it stops firing and then run up and hit it with heavy weapons. Past this mess are two more bazooka soldiers (64%) and a missile launcher that has to be destroyed with lock on weapons (65%). Once you try and move onward your way will be blocked by energy fields and a radar dish will drop down. Destroy it before it fires on you (69%) and you won't have any problems.
Move around the island in the middle and take out the turret right behind it (70%) and the two snipers on either side (71%). First head down the right side and destroy the searchbot, sniper, and missile launcher (75%). Now head back down and destroy the same enemies on the left (79%). Move past the side guns when they aren't firing and kill the two snipers and two armored soldiers at the far end (83%). Once the big missile launcher opens up, destroy it (85%) and the battleship will be defeated.
Boss: Animal Contra
- Standing at the end of the battleship is Animal Contra, a dog. He announces that the ship is about to self-destruct and jumps aboard his escape pod. Bill and Jaguar grab two torpedoes and jump down after him.
Make sure you destroy Animal Contra's laser cannons (95%) before going after the body (100%). It's hard to hit the body, but easy to avoid the laser cannon, so just have patience.
- Animal Contra's boat explodes, launching him into the sky, never to be seen again.
Your progress so far determines what happens next:
- If you haven't finished all four stages you will be dumped back onto the main menu regardless of play mode and ranking.
- If you've finished all four stages on easy mode the game is over, and you'll get a message telling you to play again on normal.
- If you've finished the first four stages and have an overall ranking of D, the game will end. All you get is a message telling you to get a higher score.
- If you've finished all four stages and have ranking of C or higher Stage 5 will now appear on the main menu.