On every Hellflower Missile turn, I would have ordered global "hit the deck" actions. Getting behind cover would have resulted in waging a battle with the Battleflower across the school, with it demolishing it piece by piece with each missile until it was dead or the school was reduced to rubble. At other points, you could have cut open water tubes to hit the Battleflower and its Pods with an AoE attack, collapsed the ground beneath it to reduce its HP, and so on and so forth.
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Currently playing: League of Legends, Chrono Cross.
Current Projects: Fool's Overture, CYOA: http://www.gamefaqs.com/boards/8-gamefaqs-contests/60143513