Mario and Luigi Partners in Time Boss Guide
If you have ever been stuck on a difficult boss battle, or cannot for the life of you get past the final form of the Elder Princess Shroob, then fear no longer! The generic idiots guide to beating the boss characters in this game is here and you should soon be able to walk right over any boss you ever need to face!
Important Notice: The below strategies are recommended by myself personally, but since the Red Shell, Trampoline and Copy Flower can keep going forever, you can technically kill an enemy, 1 hp at a time without paying any attention to what I am about to say. But the strategies will help non saints beat anything difficult they face.
Ignoring the Baby Bowser/Shroob battles, as they are pre-programmed so any normal person will win.
Leet Hammer Bros
If you don't know why people refer to them as leet Hammer Bros, please learn a bit about internet slang and watch the cut scene video posted on Youtube, or get to this part yourself.
Okay, to actually defeat them, you must remember that you have no adult Mario or Luigi to help you in this battle, and you are playing as the Baby Bros. This gives you a great speed advantage, but a pretty bad disadvantage in power and defense, so make sure to dodge their attacks.
One hammer attack used is simply to throw the hammer in a straight line. Just jump as it is about to reach you to dodge this relatively simple attack. The other is pretty simply just throwing a hammer that bounces overhead. Do not jump at that point. You should generally win pretty easily though, with or without help.
Swiggler

Ever so named as it is an alien wiggler enemy which drinks a glass of green fluid, you must remember not to attack when it is in the normal form. This is because not only will you do a lot less damage, but he will counter attack by causing a shockwave which you then must jump.
To win, you must first wait for one of the smaller Dr Shroob enemies to carry a grey mushroom. Now attack this monster, and the mushroom will fly into the drink, which is drunk then by Swiggler, causing it to be poisoned, not attack and it's defence get greatly lowered.
Now just blast away with all the powerful Bros Items (you do have some, right?) and you should eventually win pretty easily. However, DO NOT attack one of the Dr Shroob enemies if they are holding a normal mushroom! This will cause the Swiggler to be healed by the item, and waste valuable time.
Kamek

Well, this was an expected boss to fight anyway, but this magikoopa sure is an annoying pest to face in battle. I really don't remember all of how to dodge his attacks and smash this boss.
However, a good tip is that when the boss splits into four versions of himself, use multiple attacks to hit the boss, so you are guaranteed to hit the real version, and make the clones fade away into nothingness. Then, you should get another chance to attack, so hit him with a very powerful bros item then.
Sunnycide

After coming across this strange freak of a monster (what the hell is it anyway?), you may be a bit intimidated by the difficulty of the battle. So remember, keep calm and it will all be fine if you just follow this short strategy.
The main thing to do is dodge his egg throwing attack. So prepare to jump shortly after the crosshair aims at a character to dodge the flying egg that will shoot to the right.
The next thing is probably his most annoying, and hardest to dodge attack. Sunnycide will suck in a random brother, and you then have to hit the creature in the face with the hammer when you get near, otherwise he'll eat that character and take away some health, restoring his own in the process. This is pretty difficult to avoid, but try not to get eaten too often.
Now to destroying the thing. As you can clearly see, there will be about six eggs in front of the boss at all times, and to weaken his defence, you must use them to your advantage. Quickly take out as many eggs as possible with powerful attacks, then a Yoshi should appear out of each one, and run off screen to the right. They will then appear on a ledge pushing a very large chain chomp shaped boulder, and when five are gathered, throw it at the boss. This will cause him to not be able to attack, and you to pelt the creature with as many powerful attacks as possible, as his defence will have decreased. Keep this up until you win.
Shrooboid Brat
Seeing as this battle is very simply a matter of dodging it's one real kind of attack and pummeling the creature before you take too much damage, I will just get to the actual point.
The main attack is firing the weapon he is holding at the Bros. So remember, watch the audience and be prepared, as he is not just going to aim at one character.
When he is about to attack, he will face the audience of Shroobs in the background. If they mainly hold up cards with M on, prepare to jump with Mario first, then Luigi. If they hold up cards with L on, prepare to jump with Luigi first, then Mario.
For attacking, your best aim is to hit with as many easy to use and powerful Bros Items you can. He should fall pretty quickly if you follow these instructions, as his attacks are rather limited.
Petey Piranha
Yes, he is literally the most hated character in all Mario games past and future, and the one that 90% of players wish was never created in Super Mario Sunshine, but this jerk has supposedly eaten Princess Peach, and a few other characters, so you'll have to fight the creature anyway.
One of the first things he will do is to fly up to the top screen and dive at the lower screen. The pattern is that if he falls head first, Mario will have to jump (then Luigi) and if he literally barrel rolls into the ground, then both characters will have to jump to avoid the attack.
First you must remember that ground based attacks cannot hit the boss in his flying state, and that you have to stick to attacks which will hit enemies who are in the air, such as Cannonballers, Trampolines, Copy Flowers, Mix Flowers and certain attacks from the Fire and Ice Flowers (mash X or Y instead of A or B).
Later in the battle, a drastic change will take place. The plant will dig into the ground, and pretty much stay there for a while, exposing it to ground based items. However, now it is treated like a spike topped monster and jump attacks will do damage to YOU if you attempt to use them against the boss. So now it is time to unleash the Mix Flowers, the Ice and Fire Flowers and the Shells to damage the boss in a non jump based way.
Petey will later start causing the sand to go towards him, so keep jumping to avoid being dragged under the ground and losing health. Another attack is a piranha plant on a vine, which will swing back and forth between each character, forcing you to smash the thing until it eventually breaks away.
All in all, the boss using ground based attacks is much easier and safer for you than when it is flying, so as soon as it reaches that form, unleashes every non jump attack on the beast immediately!
Mrs Thwomp
Angry at you making Thwomp Volcano extinct using a whole load of water from the future, this stone creature is the next annoying foe to have to face in battle.
One attack is throwing rocks, quite simply, so be prepared to hammer them away with both Bros to avoid losing a small section of health. Another is the shockwave attack, where you must jump with one brother then the other, or just both at once twice.
Sometime in the battle though, the boss should split into four. So look for the one Thwomp without something different in it's design, and you will have found the real boss. Attack that with as many powerful attacks as you can manage. Repeat the cycle of the boss using attacks, splitting and attacking the real one until you win. I didn't have much trouble here either.
Bowser and Baby Bowser
In the place where each one says they want to build a second castle, right at the bottom of the Thwomp Caverns, you will find this pair. After much arguing and calling each other imposters, they will soon team up and attempt to destroy the group.
First, Bowser will use his normal fire breathing attack, so prepare to jump with both (I know, he only flames one, but jumping with both is helpful here, as there is no follow up attack). Howevever, if he stops and grins in front of one character, jump about a second or so later, after he has stalled the attack.
Sometimes, he will spit fireballs a different way. Baby Bowser will leap off the screen, and come down on Bowser, causing fire to be shot at the brothers. So jump with both, especially when he leaps high off the screen. This attack is often used a few times in a row, so be ready!
When Bowser goes into his shell, prepare the hammers. Hit the shell which gets faster between the brothers, and eventually you should smash it off screen, leaving on Baby Bowser on the screen. Use this time to badly damage Baby Bowser with your powerful Bros Items, and if you can kill him quickly, he won't be able to help Bowser when he returns.
Finally, keep hurting them until you eventually beat them. It's tough the first time, but keep trying and eventually you'll smash the heck out of these two soon enough.
Commander Shroob
Being a coward, this shroob will use three Support Shroobs to attack Mario and Luigi. Remember, you cannot really damage the Shroob-omb badly, so don't try (unless you are extremely good at infinite hit attacks or something).
First, focus on hitting the shroob right at the back. Once he is killed, you will see the other two go a bit of a different colour, and finding it difficult to keep holding the Shroob-omb.
However, you will probably get attacked a few times, so be prepared. One attack is to throw the Shroob-omb at Mario and Luigi. Use your hammers to keep batting the Shroob-omb at the Support Shroobs, and it will eventually explode in their face, causing them some damage (and from some UFO, another Shroob-omb will get brought into the battle). The other attack is their basic charge, so simply avoid the attack by jumping them.
Once you have killed the centre and right Support Shroob, the Shroob-omb will roll to the right, causing the Commander to be thrown into the battlefield. Now is your time to really cause some damage, and damage this jerk (as he's your target).
He will sometimes use his laser weapon, so simply jump the shot like against a normal Shroob enemy. He will also throw Shroobs at you, so knock them away with the hammer. Eventually, he will call out more Support Shroobs, so repeat the process and battle the Commander until you win.
Elder Shrooboid

After the cut scene involving two important characters being turned into purple mushrooms in about a milisecond, you win have to fight this very strange monstrosity.
The first thing you must note, is that you cannot do any major damage to this boss as it is! Each attack will simply do one damage, and unless you are very good with trampolines or copy flowers, you won't win this way.
So you have to dodge the fireball attack it uses, and wait for the key attack- the spiked rolling ball. Hit this away with your hammer so it flies into the air, and somehow, don't ask why, the Elder Shrooboid will fall on it's back. So now pummel away with powerful Bros Items to destroy it before it gets up again.
Later, it will call a UFO, with a timer. Do not let this run out! If you do, I'm kind of assuming you get blasted to heck and get Game Over, having to restart the whole battle again! So hit the UFO to reset the timer by hammering the spiked ball at it with Mario, and also causing the Elder Shrooboid to fall over at the same time. Repeat this process until you easily destroy this boss.
Princess Shroob Battle Form 1
If you are slow starting, jump the rings fired by the machine used used the Shroob Princess, then hit the machine with the hammer to avoid getting crushed. Then, weaken the Force field using the infinite hit power items such as Copy Flowers, Trampolines, etc.
Eventually, the force field will break, so unleash every possible power Bros attack you need, and you will eventually defeat the boss. Jump the stars she fires if you are about to get attack, and keep repeating the process with the force field until you get a quite easy win.
WARNING: Mass Spoilers below
Watch the cut scene where Princess Peach says something about the Cobalt Star, Baby Bowser screws up after trying to steal the treasure and the Elder Princess Shroob appears after turning him into a mushroom.
Elder Princess Shroob Form 1
This first part is extremely easy, so I will just say to use as few items as possible here, as the attacks are less devastating than the final form. First, you will get given a star to shoot down some UFOs, so do so and hope you get a free item (a shell or fire flower is common). Now, she will do one of three possible attacks:
1- She'll fly into the background and shoot fire. Jump the attacks, and when she shoots them directly out the screen, jump if they are fired when she is hovering low and stand still if she is floating a long way up the screen. When she lands, a shockwave will get fired, so jump it.
2- She'll get a large meteorite, so repeatedly hammer her to send her away. This is a good option, as you can cause anywhere up to 200 damage just by counter attacking.
3- She'll get healed. Then, she will likely bring a Chain Chomp into the arena, so jump it's charges around and hopefully land on the beast to destroy it and end the attack quicker.
When you get a turn, use a powerful item to deal hundreds of damage. But be warned, she will then charge at one of the Brothers, so hit her with a hammer until she backs away.
Note: When she is weak, she will heal more often. And try to have high health, otherwise Princess Peach may throw a mushroom rather than a star, which lets the boss use more powerful attacks as you cannot take out the UFOs.
Elder Princess Shroob Transformed
First, you will likely NOT be faster than the boss, unless you've raised your speed stats by quite a lot beforehand. So you will likely have to dodge some attacks. For one, some tentacles may glitter, so jump or stand still with the correct brothers to avoid their stabbing attacks.
Then, one or two may go slowly towards the brothers, so hammer them away or take a lot of damage.
Finally, the legs will spin around, so jump with each individual brother first. Then, jump with both Mario and Luigi when they spin really quickly.
Now, on your turn, use a Mix Flower. Make the fireball as powerful as possible to destroy all the tentacles, the feet and about 1 hp of the actual boss. This will make the crown possible attack, so send every tough item you have at the crown. Eventually, when it smashes, you can harm the boss properly.
Here, fire EVERYTHING possible. Cannonballers, Trampolines, Mix Flowers, Copy Flowers, Shells, Pocket Chomps. Unleash it like it's your last turn (it isn't, but that may encourage you a bit). All though if you had the Ulti Free badge, every attack SHOULD have been a Bros Item anyway.
Eventually, the crown will reactivate, so keep attacking it, and destroying tentacles and feet when they reappear. You should eventually destroy the boss and end the final battle quickly. It's all over... you think...
Shrowser
Uh, Bowser got possessed AGAIN? After getting possessed in Superstar Saga he gets his body hi-jacked by the Elder Princess Shroob? Well, ignoring the idiocy of the not so as evil as he thinks common Mario arch enemy, this 'boss' is more like a mini game than a battle...
First, you are NOT attacking Shrowser! You don't get to, and he deflects every counter attacked shot upwards. However, you are causing the life bar of the spirit of the Elder Princess Shroob to go down by dodging and counter attacking the boss attacks.
First, he will probably shoot fire. Just jump for it to go off screen, loop around and hit the Princess Shroob soul in the face.
His next attack is breathing tons of fire. The spirit of Elder Princess Shroob will point with a different tentacle to show which brother the attack is aiming for. Left means Mario, right means Luigi.
The final attack is breathing a huge fireball which goes directly at one of the characters. The same aiming as the second attack applies, so watch carefully and smash it back with the hammer. Note that the fire gets larger as the battle progresses.
Finally, you should deplete all the health bar and defeat Shrowser! You've finally won the entire game!