dddThisseasonbeganmerelytwowholeweeksafterthefirstseasonhadended,onApril19,2008,withtheairingofTheEliteGuard,andendedonJuly5,2008,withthetwo-parter,ABridgeTooClose.TheseasonrevolvedmainlyaroundtheAutobotsintheaftermathofMegatron'sreturn,tryingtorestorethecityandtheirimage.Meanwhile,Megatron,Lugnut,andBlitzwinghavecapturedProf.SumdacinordertobuildaSpaceBridge,hopingtouseittoconqueraweakenedCybertronfromwithin.Asub-plotalsofocusesonSariasshesearchesforherfather,whilelearningthatthereisnorecordofherexistenceofanymeans.Also,Blackarachnia(originallyElitaOne)hasbeenreducedtoaminorrecurringcharacter,onlyappearinginoneepisodeoftheentireseason(BlackFriday).

bbbThethirdseasonbeganonMarch14,2009withthethree-partpremiere,Transwarped,andendedonMay23,2009.ThisseasonfollowingtheeventsofTranswarpedfocusedontheAutobots'attempttoreachCybertroninordertowarntheAutobotHighCouncilofShockwave,whohasbeenmasqueradingasAutobotIntelligenceOfficerLongarmPrime.Meanwhile,Megatron,Starscream,Shockwave(whoreplacesBlitzwingasamaincharacter),andLugnutplantousethecolossalAutobotOmegaSupremeforconstructingclonesofhim(dubbedasLugnutSupremes,astheyappearsimilartoLugnut).