The Doorknob will greet you here (this is what I mean when I say that this movie is a bit stranger than most other Disney movies). You can drink one of the drinks on the table to shrink small enough to fit through the door. What door you ask? Well, before you drink the bottle, check the bed, and push it into the wall. This reveals the doorway. Now you should drink the bottle and head through the door.
Enter Alice and the Queen of Hearts. Alice is on trial for attempted theft of the Queen's heart, and she is pretty much helpless. The Queen only does things that are convenient to her, and Alice is the easiest person for the queen to lay the blame on. Sora decides to help out, so you're stuck searching for evidence. While you're here, you can continuously talk to Alice for some interesting conversations. Keep talking to her until she repeats herself. Save at the Save point, and then take the door to the Lotus Forest (left of the Queen).
Here in the Lotus forest you will meet the mysterious, very cool looking Cheshire Cat, but he tends to talk in riddles, so he can be more annoying than helpful. He still is the coolest character though! There are four pieces of evidence. You only have to find one, but it is very beneficial to find all four of them. Start by searching the small alcove to the right. If you walk straight forward from the door that you came in, you will walk past a red flower, and the alcove is right there to your right. There is a small pink chest containing FOOTPRINTS, which is one of the pieces of evidence (footprints in a box?). There is also a Trinity mark here as well. Use it to obtain a POTION, an ETHER, a TENT, and some MP balls. You can also give the flower a Potion for a HI-POTION and more MP balls.
There are also a couple of red flowers, the one near the entrance, and one on the other side of the forest. Give them both Ethers to get a CAMPING SET from each one. Do this only if you have some extra Ethers. These flowers also spit out HP balls.
Back in the alcove with the Trinity mark, jump up the mushrooms until you reach a door on the side of the big tree. This will take you back to the Bizarre Room. You will land on the fireplace next to a chest containing the STENCH. Just two more pieces of evidence!
In the back of the forest, past the second red flower, are more mushrooms. Jump on the little one, and then jump on to the mushroom to the right. From here, you can see another evidence box. Jump across to it, and open it for an ANTENNA. Look to the corner of the room to see a blue chest. The jump to the ledge is really hard, but Sora will grab on if you jump at the last possible second while running off the edge. The chest here contains a THUNDER-G. Back at the bottom, jump on the small mushroom again and then jump to the left. There is a chest here that contains DALMATIANS 16, 17, and 18. Congrats!
Back at the entrance, look for the other yellow flower next to the fake lake. Give this one a Potion to grow bigger. Step on the nearby stump (right next to the entrance, you'll get the message "see ya") to raise a platform, and then head over to the big tree in the middle of the area. Choose to "take" the seed after examining it, but leave it on the ground. Hit the tree to change its direction, and then eat the seed to shrink again. Back in the alcove where you found the first piece of evidence, jump up the mushrooms again and follow the platforms to a new opening on the wall that leads to the Bizarre Room.
Be careful when you land! You don't want to fall off. Use the first person view to spot the last chest. Carefully jump across to it, and open it for the CLAW MARKS. The Cheshire Cat appears to give you BLIZZARD magic. Yay! Now you can blast those pesky little mages out of the air, and get Tech points for it! Now jump back down and head back to present the evidence to the Queen.
First things first: save your game. Now talk to the Cards in front of the Queen to present the evidence. The court system is still very corrupt, and you will have to choose a box that contains your evidence. There are now five boxes, and you need to choose one of them at random. The more Evidence you collected, the better your chances of getting back one of the pieces of evidence. If you choose the wrong box, Donald, Goofy, or both of them will pop out and will be put in cages. You will want them for the next fight, so it may be wise to reload if they are imprisoned. However, you can break the cages that they're inby repeatedly striking them.
As soon as everyone realizes that Alice is gone, another search is put upon the group. You must find out where Alice went! Don't worry about being attacked by the cards again either. It seems that all is forgiven for the time being! If you return to the Rabbit Hole (where you entered) you can fight some enemies to make a chest with a MEGA-POTION appear.
Back in the Lotus forest, feed the yellow flower another potion to grow large. Slide the nearby boulder into the pond to raise two mushrooms. Hit the big tree to access the nut again, and choose to take it. Before eating it, hit the tree again to keep it facing away from you. Now eat the acorn to shrink back to small size.
Back at the pond, use the newly raised mushrooms to access a closed off area. Feed the yellow flower a Hi-Potion to receive a MEGA-POTION and some MP balls. Use the Trinity mark to get a CAMPING SET and even more MP balls. Ignore the bellflowers for now, and enter the nearby door to find yourself back in the Queen's Castle. Open the nearby chest for an AERO-G. From here, drop down and reenter the forest.
Back in the forest, head to the back again, and jump on the mushrooms (use the larger mushroom on the left) to reach the branch with the acorn. From here, enter the nearby door set into the leafy canopy to enter the Bizarre Room... but I think Bizarre Room is a gross understatement for what you find next. The whole room has been turned on its side! Check the first lamp to light it, and you will receive a chest with a DEFENSE UP. When you light the second lamp, a picture appears. Examine this to reenter another closed off section of the Lotus Forest. Feed a Potion to the flower on the right to get a HI-POTION and MP balls. You can give the other flower an Elixir for a MYTHRIL SHARD and some munny, but it's up to you whether or not you make the trade in. You'll get about 180 munny for this. Exit this section of the forest the way you came in.
Back in the Bizarre Room, examine the shelf with the teddy bear, and attack the latch to make the shelf drop the bear. This affects events a bit later. Exit the Bizarre Room the way you came in.
Here in the forest, go back to the entrance, and jump up the mushrooms in the alcove. Head up toward the door above the entrance, and you will exit back out into Bizarre Room, this time on the other wall. Turn the faucet to make the pot become real, and jump into it to return to the Queen's Castle area. The nearby chest contains DALMATIANS 58, 59, and 60.
Save here, and return to the Bizarre Room (right-side up), and grow big again. The book that appeared in the corner contains a MYTHRIL SHARD. Move the teddy bear to the other chair to create a clock. Move it to reveal another entrance. Turn small again and exit to the Tea Party Garden.
When you enter, take the AEROGA-G from the chest and hop down. Read the sign near the portrait a couple of times. You can sit in any of the chairs once, and 5 of them will yield very good items. The other two trigger battles that you may or may not wish to fight.
Now enter the door nearby that leads to the Bizarre Room. Now you're on the ceiling! Jump onto the table from the nearby ramp and light the candles to talk to the Cheshire Cat again. Down on the wall is a small latch that opens a hidden door. Jump through to find yet another chest in the Queen's Castle area. This one contains DALMATIANS 13, 14, and 15. Nine down, ninety to go. Yipee!
Enter the Bizarre room again (right side up), and check the plant to get a couple of POTIONS and a MYTHRIL SHARD, as well as some HP balls. Make sure to go back into the Queen's Castle area to save before talking to the Cheshire Cat. You should be around level 13 if you want an easy battle. An IFRIT'S HORN is yours for completing this battle.
Following the post-battle cutscene, you will receive a NAVI-G PIECE, and that's about all that's left to do in Wonderland, for now.