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The second-in-command refers to a Transformer whose status is second to the commander's. A Transformer who is second-in-command is not necessarily ranked Sub-Commander, while a Transformer ranked Sub-Commander is usually the second-in-command. The rank generally varies between factions. For the Autobots and the Maximals, the rank is usually overlooked, but it still receives its own holiday. For the Decepticons and Predacons, choosing a Second-in-Command is a very tough decision. Pick one too loyal, and everyone will ignore him. Pick one too bold, and the leader may find himself scrapped.
- Grimlock 
- Prowl 
- Jazz 
- Jetfire (Unicron Trilogy)
- Ultra Magnus 
- Ultra Magnus (RID)
- Sentinel Prime (TFA)
- Ultra Magnus (Prime)
- Jazz 
- Jazz (Movie)
- Prowl - Lieutenant of Sentinel Prime 
- Red Alert (Armada)
- Slingshot 
- Sky Garry
- Waver - Second-in-command of Multiforce
- Ratchet (TFA)
- Jazz (TFA)
- Alpha Trion (Animated)
- Slag - Second-in-command of the Dinobots
- Ratchet (Prime)
- Scourge (RID)
- Shockwave (Animated)
- Scorponok 
- Shockwave (Movie)
- Starscream (Movie)
- Thundercracker (Movie)
- Starscream (TFA)
- Shockwave (TFA)
- Starscream (Shattered Glass)
- Starscream (Prime)
- Dreadwing (Prime)
- Dinobot (BW) - Original second-in-command to Megatron before he joined the Maximals.
- Inferno (BW) - Second-in-command (after the death of Scorponok)
- Scorponok (BW) - Second-in-command to Megatron after Dinbot's 'departure' from the Predacons.
- Jetstorm (BM) - Second-in-command to Megatron
- Thrust (BM) - Second-in-command after Jetstorm was reformatted back into Silverbolt
- In Prime, Megatron states that Dreadwing will make a fine second-in-command after Dreadwing countermands Megatron's orders and ends up saving Megatron in the process. This may mean that Decepticons expect their lieutenants to betray them at some point as a test.
- This bears a resemblance to the Sith of the Star Wars franchise. A Sith Lord's apprentice is expected to one day betray and kill his master and take their place. An example of this can be seen with Darth Sidious and his apprentice Darth Maul. Sidious refuses to acknowledge Maul as his true apprentice until Maul, who was previously truly loyal, considers killing his master.