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).

1915年，面对奥匈帝国的军事优势，塞尔维亚王国国王彼得一世率军民穿过阿尔巴尼亚山区撤退，途中损失惨重

 五年过后……    台场，超乎想象的多起凶残案件同时发生！    五年过后，原本全是空地的台场地区，盖满了高楼大厦与魅力景点，摇身一变为一年有四千万名观光客造访的观光胜地。随着观光客的增殖，湾岸署也忙于处理观光导览、迷路儿童、交通整理等日常事务。此时，辖区内发生了一起变态杀人案，青岛等湾岸署警员因暌违已久的大案子顿时热血沸腾，来自警视厅的室井等人也来到湾岸署成立搜查本部，在女性管理官冲田的麾下展开搜查。但是，此时暴力案件等数桩起件也接二连三同时发生！凶恶犯罪者的魔掌正悄悄伸向青岛等人。台场临海副都心，最糟最恶的三天就这样展开了。

官方预告一个孩子来到墨西哥小镇，与当地的一个男孩建立了意想不到的友谊，而一个黑暗的秘密将他们永远联系在一起。