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).

昭和29年の「ゴジラ」でスタートした東宝の怪獣映画シリーズは、「モスラ」や「妖星ゴラス」などの傑作を生み出し、また「大怪獣ガメラ」や「大巨獣ガッパ」など他社の怪獣ものにも影響を与え、海外にも多くのゴジラ?フリークを生み出した。しかしそのマンネリ化は防ぎようもなく、昭和40年代に入ったあたりから初期の頃のヒューマンな味わいが薄れ、怪獣同士の戦いがメインの子供向け作品に移行していく。この作品はそれまでの東宝怪獣キャラクターが勢ぞろいして怪獣島に管理され、平和な生活を送っているという状況で物語が始まる。そこに宇宙から凶悪怪獣キングギドラが飛来し、地球怪獣との死闘が……。

在一个迥异鬼魅的社会，上百层的高楼大厦拔地而起，俨然构筑了一个全然封闭的城市乡镇。居住在138层的女子高中生藤崎（藤崎露琪诺 饰）此前很长时间没有去学校，这一天她乘坐交通工具“移动机筒”赶往学校，不同身份的乘客相继走入，带着各异的目的去往他们的楼层。谁知意外毫无征兆发生，移动机筒因爆炸事故突然停止运行。突如其来的状况，让所有人的命运发生转变。原本甘心受戮的死囚犯仿佛窥到一线生机，因此展开拼死搏杀。逼仄的轿厢内，人间地狱骤然降临。 　　在此过程中，藤崎好像发现自己拥有某种奇特的能力，而她的命运也变得愈加扑朔迷离……