ThethirdseasonbeganonMarch14,2009withthethree-partpremiere,Transwarped,andendedonMay23,2009.ThisseasonfollowingtheeventsofTranswarpedfocusedontheAutobots'attempttoreachCybertroninordertowarntheAutobotHighCouncilofShockwave,whohasbeenmasqueradingasAutobotIntelligenceOfficerLongarmPrime.Meanwhile,Megatron,Starscream,Shockwave(whoreplacesBlitzwingasamaincharacter),andLugnutplantousethecolossalAutobotOmegaSupremeforconstructingclonesofhim(dubbedasLugnutSupremes,astheyappearsimilartoLugnut).
井口裕香,速水奖,井上和彦,高山南,寺崎裕香,森川智之,井上喜久子,梅原裕一郎,濑户麻沙美,东山奈央,子安武人,前野智昭,田村睦心,狩野翔,三瓶由布子,安野希世乃,中岛爱,小山刚志,折笠富美子,白井悠介,山下诚一郎,宫泽清子,田村由香里,小山茉美,山路和弘,福原克己