How to defeat Thunder(after you've gathered 2K+ of starting money and all upgrades are unlocked):
Buy the three best flag upgrades first, starting from the very best, then buy the best weapon upgrade. If you grind enough money, you'll be able to buy all the upgrades before facing the final boss. Oh, and make sure your dodging skill is quite good.
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 "Fade"){kind=icon}
 "Spewer"){kind=icon}