Major Spoiler/My help against the mega boss you are clearly not supposed to beat but can if you waste enough time:
My strat was growth way on sam, elephant gun in red and the watch (that gives haste) on vix, with this you have a pretty easy time beating everything before miss d, and her as well, just use growth ray on the character holding the elephant and blast her away, use vix 2 turns to apply seduced to reduce damage from enemies and heal if nedded, do that and you can beat her pretty easily