idw Ratchet is someone who follows orders and respects authority. He might follow his conscience in spur-of-the-moment decisions that allows him the leeway/initiative to act on his own (e.g. setting up clinic on Dead End, breaking cover to save Verity and Hunter, going to look for Drift, voting against Rodimus in mtmte) but he's never openly defied the orders of an acting leader. Regardless if he doesn't agree with said order and thinks it's stupid. Or wrong.
Even when Ratchet thinks Rodimus' treatment of Drift is unfair, he never speaks up against Rodimus during the actual issue of the exile verdict. He only offers Drift silent support by helping him up on the way out, because Rodimus is the captain and you don't argue with the captain. Yes he thinks Rodimus is a crap captain and acts condesending towards him all the time but when it comes to rank and orders there's no ambiguity.
Voting against Rodimus in the crisis act is a legitimate expression of disapproval, made anonymously in private. He doesn't care about Rodimus knowing his vote, but in public it stays anonymous. He does tell Rodimus off about what he did to Drift, but again, he makes sure it's a private one-on-one appointment. He also doesn't make Rodimus formally revoke Drift's exile or sanction his search, he resigns his position as CMO and quietly leaves to look for Drift himself as a personal commitment.
Common stereotype of what Ratchet is not:
Medic ethics and commitment to patients comes first, factions be damned. I don't care if he's a Decepticon, he's my patient.
No he's not actually like that? When Megatron's in custody he's all lets dissect him awwwww why can't we dissect him why does mass murderers still get rights that's so stupid can't I just torture him a little?
Like he spent the whole war patching up Decepticon-inflicted wounds and witnessing Decepticon-inflicted deaths. He's not a saint. He has as much good reason to hate Megatron and his faction as any other Autobot.
In fact he was pretty eager to ask Optimus about what he's going to decide as Megatron's punishment after he heard about Optimus frying Megatron on the voltage harness.
Optimus has his heart on clemency. Ratchet's the one hoping for execution or something equally nasty. Even though their opinions doesn't line up, Ratchet's still 100% supportive of Optimus' decision.
He repairs Megatron only because of Bumblebee's orders, and makes his unwillingness known.
Later in mtmte Ratchet does save Megatron's life of his own volition and repairs him again, but that's after he's lived with Megatron on the same ship for six months (again something that he considers to be a colossally bad idea but is forced to live with because of orders) and got to know him as a person. Not because of bleeding heart syndrome.
Also Ratchet's not just a grouch all the time. He can be blunt but also knows when to be respectful as appropriate to the occasion. He reprimands Wheeljack for being disrespectful to Bumblebee because leaders should be treated like leaders.
The guy's been CMO since Nominus Prime, essentially the highest-ranking of his profession on the planet; you can't get to that type of position and hold it through consecutive leaders for millions of years without considerable interpersonal skills and knowledge of social protocol.
Prowl does have Ratchet on his little blacklist but the stuff on there really just refers to Ratchet saving Verity and Hunter back in Infilitration. I read it as more of a testament to Prowl's pettiness than Ratchet actually being a problem.
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