What part? If you mean fighting mother brain, what you want to do is alternate between standing on the platform where the capsule used to be, and standing on the platform under it.
Shoot from the capsule platform until the 'spagettios' get too close. Once they do, jump down on the lower platform, and either wait for the spagettios to pass, or kill them. Make sure to alternate between the two spots on the lower platform, as the missle launcher can hit both spots. Just stand in one spot, and then move to the other when the missle shoots.
