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Did he get both arms cut off? If not, it could be Fullmetal Alchemist.
Edited by GitarooHero Saving the world, one fret button at a time.
Are you using "old" as in "1990s and before" old or are you implying 2000s anime are old? It doesn't sound like Fullmetal Alchemist to me. I guess you could say Ed saved Rose, he had one arm removed, and he did find out that Sloth was based off his mother and but it doesn't really sound like FMA.
I wouldn't exactly call 2007 "the early 2000s" either :P Anyway, if you're sure it was Toonami, knock yourself out? https://en.wikipedia.org/wiki/Toonami#Programs_list
Looking for an anime that aired on adult swim (toonami) in the early 2000s (like around 2007) and was about a "dark hero" protagonist that saved a girl from bandits, he got his arms cut off and then later found his mother that knew he was already dead. The details are fuzzy because i was about 8 at the time.