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

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