When you're ready to end your epic adventure, head for the crater in north-western part of the world. Save your game when prompted.
The final battle will begin with a third mechat mini-game, in which you are to shoot down the enemy Land Shark. The controls are the same as before. Doing this will be easier, due to mechat upgrades you (hopefully) installed.
Mecha Robo Cube
Land on the cube to the left. You'll meet your old pals from Baroy there. Near the ship there is a chest with MP Boost Elixir and Toripo. Activate the teleport here. Or, look for two black barrier chests (Mega MP Up Elixir, Mega HP Up Elixir), as well as some other, minor goodies. You can use the shops here and get healed by the droids. When you're ready, hop on board and fly to the other cube.