Car running bad and dieing

[Blue Flame V6]

Ok I haven't been driving my car much lately. Well yesterday I went to take it to get some stuff cause I was working on my jimmy. It would start battery guage was low so I was like ok just ran the battery down don't know why no big deal so I have my roomate push it and pop the clutch and its backfiring won't rev knocking has reduced power light on and it is stuck in limp home mode. So we push it out of the street and I bust out my hypertech and reset the computer and now it runs fine. Anyone have any ideas what would have caused this?