A year after assuming leadership of the Autobots, Rodimus Prime hosts an intergalactic sporting event, which falls victim to an attack, resulting in the abduction of Spike Witwicky, Kup, and Ultra Magnus. Rodimus is quick to blame the Decepticons, who are divided and weakened by the loss of their leader, Galvatron. But Galvatron's fellow reformatted Decepticons, Scourge and Cyclonus, may have found a way to restore their leader to power. The real culprit may be a new face, but one with a link to the histories of both Autobot and Decepticon, manipulating both sides to take their own revenge.

故事讲述两派来到地球后，因为发生了一些“事件”，导致双方外形大变（也解释了两系列风格不同的原因）。也由于这些“事件”，变形金刚要隐藏于人类社会之中。如何去平衡一切关系是擎天柱作为领袖将要面临的考验，本作品的标题也由此而来。 值得一提的是，本次两派领袖 擎天柱 和 威震天 的配音者是久违的梦幻组合：来自初代动画的 Peter Cullen 和 Frank Welker！他们在阔别电视版的变形金刚作品多年后，再次一起回来共演这双经典的死对头！

Having destroyed Optimus Prime, Megatron believes that his victory over the Maximals has been accomplished, until Prime's life is saved by a very unlikely source. The Maximals rush to save their ancestor, which means putting his spark into the body of Optimus Primal, thus upgrading him to “Optimal Optimus.“ In this state of vulnerability, Megatron orders the destruction of the Maximal base, thus forcing the Maximals to move into the Ark to forever protect their ancestors.

A visit to Bumblebee's old Autobot base reveals a dangerous new enemy with an agenda of his own.

The Autobots return to Cyberton in order to restore their world to life with the Allspark, only to find the Decepticons lying in wait.

博派现在必须和极限动物并肩对抗狂派，狂派则与掠食金刚联手，拼命找寻下落不明的火种源。然而，黄金光碟却掌握在掠食金刚的手中，这款难以捉摸的文物不仅跟密卡登切身相关，还能赋予他强大的优势，用来压制死对头柯博文。这场最终之战将决定赛博坦的未来，究竟哪一派人马能胜出？

博派现在必须和极限动物并肩对抗狂派，狂派则与掠食金刚联手，拼命找寻下落不明的火种源。然而，黄金光碟却掌握在掠食金刚的手中，这款难以捉摸的文物不仅跟密卡登切身相关，还能赋予他强大的优势，用来压制死对头柯博文。这场最终之战将决定赛博坦的未来，究竟哪一派人马能胜出？

The third season began on March 14, 2009 with the three-part premiere, "Transwarped", and ended on May 23, 2009. This season following the events of "Transwarped" focused on the Autobots' attempt to reach Cybertron in order to warn the Autobot High Council of Shockwave, who has been masquerading as Autobot Intelligence Officer Longarm Prime. Meanwhile, Megatron, Starscream, Shockwave (who replaces Blitzwing as a main character), and Lugnut plan to use the colossal Autobot Omega Supreme for constructing clones of him (dubbed as Lugnut Supremes, as they appear similar to Lugnut).

擎天柱、热浪、巨石、追踪和刀锋相继通过扫描获得了恐龙形态，在一次次救援行动中逐渐学会了控制并使用这种新的形态。同时在这一季中，擎天柱把老战友海潮请来，对救援汽车人进行海上救援的训练。之后不久，又有新的塞柏坦伙伴——打捞和啰嗦加入到救援队列中来，他们之间又会碰撞出怎样的火花呢？