step 1: don't get hit
step 2: repeat step 1
also if possible, try to get the muscle doctor to spawn his bats when you're one tile above where he's standing; it will let you get rid of most of the bats without having to jump
Actually missles are so good that i can beat him before he tries to either do the attack when hes in the air and tries to shoot projectiles everywhere,or before he can spawn the bats.
During Misery's fight, equip the Blade and touch Misery's entity for 1 damage, this should help lowering the Blade to level 2 which works better for consistent damage at a higher DPS. Use the lvl 2 Blade on her first-ish phase since she'll have no orbs surrounding her, for the other 2 phases with the orbs, just stick to the Snake and kill the Bats while dodging her attacks. Her attacking phase - that isn't the lighting balls - is, energy stream, energy stream, block, repeat.
For the Doctor, just waste away at him with Missiles. Make sure to keep your distance and don't expend all of your Missile too much, the Red Crystal can blocks lots of damage if in your way, the same applies to any weapon attacking him. If he happens to go into his crouch form in the air, keep your distance and focus on the red energy streams flying all over the place, they dissipate as soon as the Doctor fires his next DNA-energy-stream. For the Muscle Doctor, keep your distance and lay waste with Missiles, and I do mean distance with 3 hp.
As soon as the Undead Core fight begins, fuck up Misery with a level 2 blade, like turn your hands into razor blades fast. Because if you kill Sue first, Misery will begin spawning goldfish missiles which are a bigger pain than Sue herself. Be careful though, because once you finish off Sue or Misery, the Undead Core starts up ahead of time and begins wrecking his usual havoc. Stay clear of the asteroids on the ground as you wail on Sue during her benign phase. She does attack, wait, phase through for distance?, wait, attack; repeat. Attack her on the phase through and wait periods and keep track of when she attack whilst dodging the asteroids and peanuts from the Undead Core.
Once those 2 are down just take out the Undead Core, during his asteroid phases, just knock him on the head with the Blade, or Snake for long range combat. During the peanuts, stay on the ground or use the Snake for long range attacks, avoid the peanuts. For the last part, just stay on the ground, dodge the asteroids and keep below from the 3 balls of light - akin to the original Core fight - that he'll fire in succession. Keep that up and you should win.
For the bats mutated Misery fires, have the Blade equipped to wipe them out quickly, but don't be afraid to take a hit since they only do 2 damage, you can regenerate that quickly if you wail on the bays long enough. The peanuts is something you gotta telegraph, just figure out where they fire from and have some good reaction timing. For Sue, not much else I can elaborate on, keep her for second, attack, wait, phase, wait, attack, repeat.