Hi, been playing with friends online, and had an alliance with AI, but for some reason the AI with his army of about 50 ships would not destroy the pirate base they were on, even though the defence of the system was at 0%. This was going on for lots of turns, and while my ally was "chilling" at the pirate base, the oponent kicked our ass...

Saved game uploaded...Kappa not taking out the enemy bases.sav

No lol, the AI invaded the pirate system, and got the system defense to 0%, but the pirate control of the system was not going away, and remained at 0% for a lot of turns while the AI and it's fleet of 50 ships were orbiting the system and ignoring the rest of the galaxy problems. I tried to bring my own fleet one time to ensure that it's actually being invaded, and it was, as I could not "double" invade it.

Could not reproduce your issue, because as soon as I load your save normally, AI kicks off pirates and colonizes the system.

Instead, I've joined the slot AI were playing to look from their perspective. First things first - they weren't invading Pirate base. They were sieging it. You couldn't invade it yourself, because it was guarded by AI.

As to why they weren't Invading that system? Hard to tell, sometimes AI can get into state loop derieved from previous states, where they prioritize one goal and ignore the other. Reloading the game usually fixes it, just like here, because AI state is recalculated based only on save data, they get a "fresh look" upon the game and "unstuck" their behavior.