Are you a member of a writer's guild? Does the indie company have any affilitation with that guild?
If not, then they can pay you whatever they want. Guilds don't protect people who aren't members and companies not associated with outside guilds don't have to abide by their rules/minimum basic contractural agreements.
I think you and this person can arrive at something that seems fair to the both of you. Do some research. Find out what other people in positions similar to yours get, then ask for that.
If something "fair" can't be reached, take your ball (script) and go home. If they want it badly enough, they'll pay you "fairly."