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).

一名大学教授的残忍谋杀案引发了学生骚乱，一位警察展开调查的同时一名律师在法庭上寻求正义。

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").

一天雨夜，青年漫画家西（今田耕司 配音）在地铁站出来遇见了初恋梦中情人弥（前田沙耶香 配音）。西送弥回家途中得知了弥已订婚，随后，他被弥邀请到酒馆喝酒，弥的未婚夫也来了，西虽然嫉妒弥的未婚夫，但自愧不如。这时，黑社会来到店里，原来弥被黑社会所追杀，打晕了弥的男友并要强奸弥，西则蜷缩一旁不敢动弹。黑社会发现了一旁的西，用枪爆了他的屁眼。前一刻，西还沉醉于与初恋梦中情人相逢时的甜蜜，下一刻就肛门中枪，贯穿脑部，死于非命。当西等人上了天堂，西觉得自己死得很难看，后悔人生过得很窝囊，决心再度复活。他们一行人违反神的意旨，并回到地上的世界，却阴差阳错却来到了鲸鱼的肚子里，接下来又将会有什么等待着他们呢……