But anyway. Transformers! Robots in disguise. This is a fandom that started as a toy line that had Bad Guy Robots and Good Guy Robots and became a sprawling sci-fi epic full of deep meditations on the nature of war, injustice, morality, redemption, personhood, forgiveness, the weight of history, etc. etc. So you can see that it would be a good one for enemy ships!
It also just has. So much canon. Like usually once I've read a million or so words of fic in a fandom, I have a pretty good idea of what has happened in it, and who the important characters are, and their relationships with each other, etc. Not so much Transformers! Also in a fandom this big, usually there is one, maybe two or three pairings that are the Large Pairings that stand out from the others. Not so much Transformers! The big ones are Jazz/Prowl (buddyslash), Optimus/Megatron (the leaders of two enemy factions finding love after eight million years of total war), and Megatron/Starscream (The leader of one faction and his mutinous subordinate who is constantly trying to overthrow him) but even the largest of them is less than 5% of the fic and there are so many other pairings.
So here are some recs, but they barely scratch the surface? There are a lot of relatively popular pairings that I rarely read because I still have only the vaguest idea who the characters are or how they fit into canon.
Also: I am not rec'cing Astolat's Transformers fics here because I want to save her for a different pairing later if I need her, but if you have any desire to read this stuff and you haven't yet, I tend to just read the whole collection under the private title of "17 Ways To End A War By Falling For The Enemy". They aren't in continuity with each other at all but they fit together as an ongoing conversation on all those things.
- Winning Hearts and Minds (and Spikes) (16625 words) by TrebleTwenty
Chapters: 4/?
Fandom: The Transformers (IDW Generation One)
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Characters: Jazz (Transformers), Prowl (Transformers), Optimus Prime, Ironhide (Transformers), Ratchet (Transformers), Blaster (Transformers), Sunstreaker (Transformers), Bumblebee (Transformers), Swindle (Transformers), Getaway (Transformers), Misfire (Transformers), Battletrap (Transformers), Punch | Counterpunch, Megatron (Transformers), Starscream (Transformers), Drift | Deadlock, Soundwave (Transformers), Shockwave (Transformers), Thundercracker (Transformers), Skywarp (Transformers)
Additional Tags: Propaganda, Hijinks & Shenanigans, Immature Sexual Humour
A very silly WIP about Autobots and Decepticons fighting a propaganda war with pin-up posters, but a fun lighthearted intro to the general setup! - The Long Walk Home (38658 words) by Spoon888
Chapters: 14/14
Fandom: Transformers - All Media Types, Transformers Generation One, The Transformers (Cartoon Generation One)
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Relationships: Megatron/Starscream
Additional Tags: Angst, Canon-Typical Violence, Injury, Nightmares, Flashbacks, PTSD, Huddling For Warmth, The Cross Country Hiking Trip Only An Idiot Like Me Would Write, Slow Burn, Sticky
Megatron and Starstream get injured and stranded, and have to walk home - across the entire US - supporting each other - and learn things about each other on the way. - House Divided (121584 words) by spaceliquid
Chapters: 28/28
Fandom: Transformers Animated (2007), Transformers - All Media Types
Rating: Explicit
Warnings: No Archive Warnings Apply
Relationships: Megatron/Optimus Prime
Additional Tags: Post-Canon, Mildly Dubious Consent, Consensual, Implied/Referenced Rape/Non-con, Implied/Referenced Prostitution, Minor Character Death (canonical), Non-Graphic Violence, Some role reversal later on, Voice Kink, Size Difference, Interspecies in a way?, Unresolved Sexual Tension, Licking, Robo knotting, Loss of Virginity, Femmes with spikes
This one is set in a slightly different continuity, where Optimus is not yet the fearsome leader of the Autobots, the war is still in early days, and at the end of canon, Megatron has been captured by Optimus and is in prison awaiting trial for war crimes and treason. But Optimus starts to see things in Autobot society that he can't unsee, and with Megatron right there, he can't leave well enough alone... - Walking the Wire (61120 words) by dracoqueen22
Chapters: 12/12
Fandom: The Transformers (IDW Generation One)
Rating: Mature
Warnings: No Archive Warnings Apply
Relationships: Megatron/Ratchet
Additional Tags: MTMTE Season Two, Sticky Sexual Interfacing, BDSM, dom/sub themes, Bondage, Trust Issues, BDSM education, Canon-Typical Violence, mentions of torture, The Lost Light Finds Trouble
So the original 80s cartoon had a follow-up of a long series of comics - several, actually, as the license was sold around - but the IDW series developed its own complicated set of continuity, the culmination of which was the Lost Light series, where a bunch of characters who had been dead in canon ended up together on a spaceship on a quixotic mission with God. (Not *from* God, just with God, he's along for the trip.) I tried actually reading this one because I was told it was very good, and was an okay starting point if you were shaky on previous canon. They were right about the first half of that? Anyway this fic is part of a series set on the Lost Light, and it's about Rachet, the Autobots' cranky old medic, getting into a complicated BDSM relationship with Megatron, who post-war and resurrection has thrown over his Deception loyalties for an Autobot badge, a very restrictive parole, and a chance at something like redemption, or acceptance, or maybe at least freedom. Anyway this fic is good! You should read it, the setup for the fic is not as complicated as I made it sound.