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The Crab Puncher attacks by punching with its giant claws, while some platforms with damaging but non-lethal spikes head towards it and destroy on contact with him. The lower claw is avoided by standing on a low platform and then jumping to a higher one, and the higher one is avoided by standing on a high platform and then falling to the floor. It also attacks by shooting bubbles, with some bubbles trying to home onto Mega Man. The player will know the Crab Puncher is going to do this because he will protect his eyes with its claws. They are avoided by running at the left and then rapidly run towards the Crab Puncher when the homing bubble approaches Mega Man (the homing bubbles will always have a yellow sphere inside it).Its eyes are its weak points, and each eye is half of the boss' health (fourteen HP each eye). The claws can be destroyed, making the fight easier. However, the claws are invulnerable if they are blocking its eyes.
Its primary weakness is the Commando Bomb, and firing it right in the middle of the boss' face will cause the explosion to hit both eyes for massive damage, hitting each eye twice. However, if the missile hits an eye directly, the Commando Bomb will only do minimal damage. It defeats the Crab Puncher in seven hits. An additional strategy is to fire a Thunder Wool above the eyes so that the lightning hits both eyes at once. Again, if the cloud hits an eye, it will be destroyed and do minimal damage. Skilled players can defeat the Crab Puncher in just one use of this weapon, which normally defeats it in seven hits. The Triple Blade at close range can also do some fair damage to it as multiple blades hitting their target can deal more damage than one blade alone. It also seems to be the pincers' weakness, as it makes short use of it by defeating it with ten blades.
Another strategy is to use the Triple Blade on the pincers until they are destroyed, and then use the Commando Bomb or the Thunder Wool to defeat its eyes.
On Easy Mode, the crab will be farther than normal, and it will shoot less bubbles. On Hard Mode, the crab will be nearer than normal, giving the player less room and time to react, it shoots more bubbles, and it will move its eyes around at different angles, making it harder to hit the boss' eyes.
- Crab Puncher slightly resembles Gazamir, a sub-boss from Phoenix Magnion's stage in Mega Man Zero 2.