Paper Mario: Master Quest - Giga Bowser

There's only one real major change in the Bowser fights in Master Quest. When Bowser's HP falls below a certain threshold (150 in this fight), he will attack immediately after using the Star Rod to go invincible. Not only can Bowser obviously not be hit when invincible, but his attack power increases significantly (I believe it doubles in Vanilla Paper Mario, but I think it's different in Master Quest). In the rematch against Final Bowser (named Giga Bowser in the Star Temple), he will use the Star Rod to go invincible after every three attacks, so you are able to predict when Bowser will go invincible. When you know he's going to go invincible, you can use Bow to go Outta Sight to completely avoid his attack, which can kill you even at full health with all defensive badges.

I brought nothing but Jelly Ultras to this fight. I tried to stall out when I used them by using Smooch instead, that way I could run my FP to near 0 before needing to heal, and getting as much use from every Jelly Ultra that I could, on both the HP and the FP side.

Also, there is a bug in this version that if you hide from Bowser when he goes invincible and he uses his triple claw+fire breath attack, he won't go back to his original position until his next attack. This can throw off some of your timing on blocking the attacks. The biggest two attacks you must block are his shockwave attack, which hits your partner, and you absolutely must block the attack with your partner or you're dead, and his lightning attack, that can paralyze Mario if unblocked. This was the most nerve-wracking part of the fight, as a missed partner block on the shock wave effectively ends the battle. Your partner will be out of commission when Bowser goes invincible, and Bowser will have you in checkmate.

The shock wave from Bowser can also remove any status boosts that you or your partner have in effect (including Water Block), so I always wait until after Bowser shock waves to put up a new Water Block, that way I get full use from it.

Finally, since Bowser heals three times, you need to get his three heals out of the way before you can finally take him down. When he heals is dependent on your percentage of your maximum HP vs. his, so I try to bait him into healing a couple of times. Until he gets all three heals in, I try to conserve my FP a bit.

For partners, Watt is the strongest member damage-wise, as she can deal 4HP using no FP. The next good bet is Goombario, who can deal 6HP with Ironbonk.