ooh, happily! These are some of my favorites:
Courtesy of Thomas Hamilton by Char7 – this one was done for me on a prompt and I still love it to little bitty pieces. It’s a take on “what if James had been sent to Bedlam instead of Thomas”
Wars Without Weapons by Shirogiku – In which Thomas saves himself from Bedlam
Never a Smooth Sailing by Shirogiku – In which James falls off the Walrus instead of Billy during Season 1 and reunions ensue
The Wind in His Sails by linndechir – this is a post-canon fic that I loved because it handles Thomas’ lingering issues from being imprisoned for ten years realistically and has him work through them a bit or start to and it’s fluffy and sweet at the same time
Revenant by Beth Winter – I LOVED EVERY WORD OF THIS FIC it is so perfect given that it’s got badass angry Thomas taking Abigail in as his ward and the two of them with James ready to burn England to cinders. I’m hoping the author does the sequel they were tossing around doing pre-finale.
a sweet light in the dark by Gedsparrowhawk – This one made me cry but it’s so, so good, and Bri, don’t think I’ve forgotten that you mentioned a sequel that would destroy me!
The New World by ESebastian – I fucking love this thing more than I have ever loved any fic that has James Flint paired with anyone other than Thomas and Miranda. It’s amazing, I adore the OCs, all of them, but especially Ezra Wake.
That should get you started, Nonny! I’m sure I can rec others, but these are all on my favorites list.