This question is especially confusing to answer for the Autobots. In More Than Meets The Eye/season 1, we find Optimus having Jazz take on duties that a 2nd in command would normally do. Things such as assembling a task force, taking role call, organizing the team, and ordering their transformations and engine starting... But then we get to season 2 and most of the time you find Ironhide assuming leadership duties when Optimus isn't around. Especially in The Search For Alpha Trion. Here Ironhide seems to be the 2nd in command, and grabs leadership if there's a situation and Optimus isn't there. In the comics, we hear that Prowl is 2nd in charge, but then later on it's Grimlock who gets to become the Autobot Leader. And in the cartoon, Grimlock seems to be the Autobot version of Starscream... he won't follow orders and does his own thing, and thinks he should lead unless Optimus Prime proves he's stronger. Then we go to Transformers: The Movie and when Optimus Prime dies, it's Ultra Magnus he passes the Matrix to, not Jazz or Grimlock, or even Hot Rod. (Ironhide and Prowl are already dead at this point so it's tough to tell what their rank truely was.) However it is Hot Rod who becomes the leader when Ultra Magnus couldn't get the job done and makes some errors of judgement. Even after Rodimus Prime becomes Prime and saves the day, Ultra Magnus has no desire to try and assume leadership back from Rodimus Prime and all the Autobots choose to follow Rodimus Prime as their leader. As a side note, it is also Jazz who is right at the side of Rodimus Prime the instant he becomes leader and helps lead the Autobots out of Unicron. For the Decepticons it's a little easier, but not totally. Most people assume Starscream is 2nd in command. And sure he did take command when it was thought Megatron was dead in season 1, but is that an oppurtunity that Starscream took, or is he actually the 2nd in command? Just because he was an oppurunist and wanted to be leader, and Megatron thought of him valuable enough to keep him around (at least until it became too much by the end of season 2), does that really make him the 2nd in command of the Decepticons? You look at all the tasks distributed by Megatron on Earth, and it seems Soundwave was always his go to Decepticon. But then again, it was Shockwave who Megatron gave the authority to rule their entire home planet. Does this mean that Shockwave is 2nd in command for the Decepticons? So the question is, who is truely the 2nd in Command for the Autobots, and who is really the 2nd in Command for the Decepticons?