This season began merely two whole weeks after the first season had ended, on April 19, 2008, with the airing of "The Elite Guard", and ended on July 5, 2008, with the two-parter, "A Bridge Too Close". The season revolved mainly around the Autobots in the aftermath of Megatron's return, trying to restore the city and their image. Meanwhile, Megatron, Lugnut, and Blitzwing have captured Prof. Sumdac in order to build a Space Bridge, hoping to use it to conquer a weakened Cybertron from within. A sub-plot also focuses on Sari as she searches for her father, while learning that there is no record of her existence of any means. Also, Blackarachnia (originally Elita One) has been reduced to a minor recurring character, only appearing in one episode of the entire season ("Black Friday").

This season began merely two whole weeks after the first season had ended, on April 19, 2008, with the airing of "The Elite Guard", and ended on July 5, 2008, with the two-parter, "A Bridge Too Close". The season revolved mainly around the Autobots in the aftermath of Megatron's return, trying to restore the city and their image. Meanwhile, Megatron, Lugnut, and Blitzwing have captured Prof. Sumdac in order to build a Space Bridge, hoping to use it to conquer a weakened Cybertron from within. A sub-plot also focuses on Sari as she searches for her father, while learning that there is no record of her existence of any means. Also, Blackarachnia (originally Elita One) has been reduced to a minor recurring character, only appearing in one episode of the entire season ("Black Friday").

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).

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).

Upon discovery of the Phantom Zone projector in his ship, Superman makes contact with and releases a prisoner whose sentence is completed.

"在这一季中，超人面临来自强大敌人的新威胁，同时深入探寻自己的氪星遗产。他不仅要对抗地球上的超级罪犯，还要面对外星势力的侵袭，尤其是来自强大的天启星领主——达克赛德。超人发现了“幻影区”并释放了氪星叛军玛拉，但她背叛了他，并释放了更强大的贾克斯-乌尔。超人不得不与这两位同族敌人对抗，并最终将他们重新封印。超人对战诸多新旧反派，包括：闪电侠联手战斗：与闪电侠合作阻止天气巫师的破坏。电击女崛起：电台主持人莱斯莉·威利斯变成电击女，成为超人新的电能对手。 超人与蝙蝠侠合作 —— 小丑与莱克斯·卢瑟联手，计划利用氪石对付超人。达克赛德全面入侵 —— 达克赛德对地球发动战争，在大都会制造大规模破坏，并亲手杀害了超人的朋友丹·特平。超人最终击退了天启星的军队，但深感自己的力量仍然无法彻底阻止达克赛德的威胁。超级少女登场 —— 超人发现了一名来自氪星殖民地阿尔戈星的幸存者卡拉，她成为了超级少女。卡拉迅速适应地球生活，并帮助超人对抗天启星的威胁。 这一季不仅展现了超人面对强敌时的智慧与力量，还塑造了他在正义与道德选择中的挣扎。随着剧情的发展，天启星的威胁逐渐升级，而超人与地球的联……

为了阻止原始兽得到行星盖亚上的神秘能源——阿古莫亚。巨无霸在白狮擎天柱的率领下，与威震天率领的机械军团展开了战斗。

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！