So is the reputation system not working?

[Happy_Puppy]

Ive been doing side missions like crazy and it tells you if you do certain ones to get a faction to like you but all mine still show 0/100

[nick1288]

From what I've understood reputation comes from contracts and instances that are available when your ego rating reaches 250. Probably their way of keeping things going, by the time you finish the main story and reach 250 this other stuff unlocks.

[Happy_Puppy]

Hmmm well I'm well over 250 more near 400 now, but I have not completed the story arc.

[Raynor]

Go into your goals menu where your pursuits are. There should be another small tab at the top of the screen that shows contracts. Those contracts are what you need to do to gain reputation. It has things like kill certain enemies in certain areas.