I've finally decided to complete this game before playing something else or I would never finish it.

When the boss is in the "open" mode where it said that you can shoot the exposed body to damage it but my beams just bounce off it.

I tried the bomb which stun it for like 1 second but nothing else.

Is there something I am missing?

Is that the boss that likes to jump around and you have to shoot the antennae?

Did you try shooting it in hyper mode?

is that when the robot guy throws your ship off the edge? I think something pops up under him. Then you morph ball under him and drop a bomb. Then you can blast the hell out of him. I thiiink..

Do a Barrel Roll!

The ones mentioned are just mid bosses?

The one I am talking about is after you dropped the bomb from skytown.

Are you talking about the boss inside the Leviathan itself, called "Helithos" or something?

If so, shoot at the core when he starts flying around, you've nearly killed him. He should now have exposed his core, and you can just hypermode and shoot him down.

He's the only boss I can think this could be. A name or location of the boss would help greatly.

go here and you will solve all your problems with the game http://www.gamefaqs.com/console/wii/game/928517.html

General rule for MP3:

If the enemy boss is lying around with an exposed core fluttering it's eyelashes and blowing kisses at you, that's your cue to inject an energy tank and hyperbeam that bitch to hell.

Helios, then. It's been a while, but i think he needs the multi-seeker missile.

Yeah that's Helios.
I actually ran out of missiles fighting it, LOL.
Didn't have time to play today, will try again tomorrow.