Beyond all reason is a large scale, fan-made, free RTS. Inspired by Total Annihilation, but most people would compare it to Supreme Commander. The maps are less huge, experimental units are cheaper and less game-ending, and building invincible shielded chokepoints is less viable, all things I think Supreme Commander went too far with. It has a lot of quality of life keybinds and the non-cheating AI feels solid, and there are enough people playing that multiplayer is also viable. I recommend 3v3s or bigger with barbarian-level AIs to make the game feel sufficiently interesting- 1v1s are still fun, but don't play into the game's strengths as much. It's in development, and the UI while setting up matches could be better, but otherwise I'd consider it's level of polish acceptable for a final release.

Starsector is probably the best space combat game around, if you don't mind that it's top down 2D. You start with as little as a single frigate and can scale up to a fleet of capital ships and several planets. The combat is designed well enough that it remains interesting for a very long time and pilot decision making has a high skill ceiling, helped by the fact that the enemy AI makes good decisions itself. Good mod support with a lot of excellent mods that add new factions and ships. There isn't a plot or any sort of main campaign missions, just general background lore, but I don't play games for their story. Singleplayer only.

If 2D is not for you and you want a space game where you pilot a ship in 3D space, try Everspace 2 for pure combat or X3 for empire building (Warning: all games by egosoft after X3 are complete trash), but I'm not sure if either of those count as indie.

AI War 1 and 2 are large scale space RTS games. The unique thing about them are that they're extremely asymmetrical- your opponent is an AI that went rogue and conquered nearly the entire human race. It starts with control of every planet in the universe except yours, and has infinite resources, but isn't actively at war with you. You don't win through direct confrontation, but by exploiting various flaws in it's logic, primarily the fact that it doesn't consider you a threat. Your "threat level" is not abstract- it is tracked as an integer and is displayed at the top of the screen, and it deliberately has a fairly predictable effect on the AI's behaviour, particularly at certain thresholds, playing into the theme that you're fighting a programmed AI, not a human. The strategy of the game comes down to analyzing the map and deciding which planets will give you tools which are worth the bump to your threat level while still maintaining a defensible front line. Both games come with several small expansions that make an already complex game potentially overwhelming, and the number of options available when generating a new game are at a level of complexity you would simply never find in a mainstream game. Learning enough to win your first game isn't trivial. This one is probably niche for a reason, but if you invest the effort, it's got a lot to offer. Can be played cooperatively if you have a friend who is as crazy as you are.

Frozen Synapse is a top-down tactical shooter, where you issue orders a few seconds at a time. During the planning phase, you plot what you think the enemy will do over the next five seconds of real time, tell your guys where to go and how to face, submit your orders, watch it all play out, then issue orders for the next five second turn, until someone runs out of guys. There are ten or so different kinds of weapons your guys can have, randomly generated maps, and a few different game modes, so there's quite a lot of variety in how the games play out. Good against AI or a person. Frozen Synapse 2 takes that and adds a strategic map to tie the combat together, but I'm not sure if it's an improvement. There's also a football variant called Frozen Endzone which I've never played.