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.
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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%).
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.
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.
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.
Your progress so far determines what happens next: