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Kill a lot of monsters, take on a lot of missions. If you want to make things go faster, use a Nano with Bonus power equipped so that you can gain extra Fusion Matter. This is especially helpful when you finish a mission; take the nano out before you finish it, let it hang while you finish, and you should get 20% extra Fusion Matter (thus, for a mission that would grant 5000 FM, you'll get 6000).