Prototype has access to three Blue Magic spells: Flame Thrower, Missile, and Self-Destruct. Only Missile and Self-Destruct can be accessed by controlling it; Flamethrower is one of the three attacks used by Prototype on its second turn, so the player will have to wait until that point to obtain it.
Prototypes can be killed easily by using Control and then having them Self-Destruct. A less efficient method is to use Off-Guard, learned by controlling Page 256, multiple times to reduce the Prototype's defenses down to a manageable level, and then attack it with the party's best spells and attacks. Alternatively, affecting it twice with Dark Spark will reduce its level to 5, rendering it vulnerable to Level 5 Death.