After the resurrection of the hero, you get the Hero's armor and weapon, and are summoned to the Lab Tower in Siberia.
Talk to the old man. Then you can go north. Meilin will disable the cameras. Wait (a while) then Meilin will talk again. Go north. In the camera room, go north again. Meilin will camouflage you so you can go past the robots. Go west and south. Go farther south and a crane will grab your head. On the other side, talk to Perel. Follow him. When he says it's all clear, go north and talk to him again. Then go east from where he's standing.
Go east and go up the stairs that you find. Go south, past the cubes, then use the west exit. Fyda will show up. Go up to the switch to the north and check on it. She'll flip the switch with you. Go south, then west, then go north to the next area. Follow the path and you will find a Magirock. Go east from there.
Go upstairs, then exit west. Go west and then use the southwest exit. Follow the path, which is straightforward, until Royd shows up. Go north through the door that he opens, then go up the stairs.
In the next area there are a bunch of red Colossus. They give the most EXP of any enemy in the game, so if you feel like grinding, do it here. You can go into the side rooms and come back out again to reset the enemies. There is one room in particular, near the bottom left, where a Colossus spawns right outside of it. Go into that room and then go out of it, doing a dash attack downward followed by a dash attack to the right, then another dash to the left to kill the Colossus. If you do it correctly, the Colossus won't hurt you and you will quickly gain EXP. You can go back into the room while the robot is exploding (you don't need to wait for the robot to disappear to get the EXP). It's best to be level 30 or more before you continue.
You can meet Meihou, Meilin, and Perel in the rooms here. In Meihou's room, there is a Life Potion. Go into the southwest room and flip the switch, then leave the room and go southeast. Go through the open door there. Then fall into the hole.
Go east into the Airship. Talk to Fyda to get Time Bombs. Equip the Time Bombs, then go to the computer behind where Fyda and Royd were. Press X to put a bomb on it.
Go east and you'll be outside. Go east and you'll be back inside. Then go north to go up some stairs that take you outside once more. Go south from there to reach another area, then go into the door to the east to get into the ship again. Go east to exit the ship yet again, then go north until you're back in the ship again. Go east to find Royd. Talk to him, then set a bomb behind where he was.
Go back the way you came until you are back at the four-way crossroads inside the ship. Go north and up some stairs to find Fyda. Talk to her, then put bombs on the two computers in this room.
Go back downstairs, then go north. You will see a path to the east and west. Use one of these exits and follow the path outside the ship until you are back inside. Go to the center of this room to find a computer guarded by two robots. Kill the robots, then plant the time bomb.
Go back the way you came until you are in the ship again. Go north until you reach two more computers. Put time bombs on them.
From this room, go south until you meet Royd and Fyda. Then go south and watch the cut scene. Afterward, go south and talk to the gull. Choose the first option. You'll land on Airsrock. Talk to the scientist. He'll say that the object looks like it landed in South America.
On your way to South America, you might want to visit a shop to stock up on L.Bulbs and whatever else you think you might need for the final battle.
Sail your ship to the east side of South America and go into the cave entrance northwest of Liotto. This is the Portal where you started Chapter 2. Go to the top of the area and talk to Columbus. If you are ready, fall into the hole.
Go to Crysta, which is just west of where you arrived. Then go north into the Elder's house and go to the Elder. If you talk to your friends in the house, they will turn into spirits that float around and hurt you. Go talk to the Elder. Follow him.
If Dark Gaia shoots an orb of light, face northward and do a rapid stab attack to knock the orb away. To avoid a sonic boom attack, stand on the far left or far right of the platform. For other attacks such as Gaia's Rage, scattered Magirocks, or if Gaia sends its upper body as a spiked ball to attack, you can do dash attacks to avoid damage. When the spiked ball stops dashing around and starts moving back toward Gaia's legs, hit it to damage it.
Dark Gaia 2
Then Dark Gaia 2 will attack. Stay at the bottom of the platform. If Gaia comes close, hit the hole in its stomach. If Gaia goes to the middle of the screen and starts drawing light into its stomach, hold L or R to block. Gaia can shoot gold orbs from its hands, so stay below the middle of Gaia to avoid these. It can also shoot silver orbs that will come beside you and then shoot toward you, so run upward or downward when they stop beside you.
After you defeat Dark Gaia 2, there will be a cut scene. After that, go talk to everybody, then sleep in your bed.
Congratulations! You won the game!