Wow, why hasn't anyone suggested Fullmetal Alchemist? Might be a little late, the original manga started in 2001 and the first animated version reached the USA in 2003 (on Toonami, I might add), but it seems close to me.
Two boys are orphaned when their mother dies (cancer is implied, though I don't recall a direct mention). Since they are sons of the greatest alchemist alive, and both studying alchemy themselves, they scheme to do the forbidden: use alchemy to bring their mother back.
Human alchemy is forbidden for good reason, though, and in the end, the elder brother, Edward, nearly bleeds to death after sacrificing his right arm and left leg to bind his younger brother Alphonse's soul to a suit of armor because the reaction has completely destroyed the younger one's body.
Edward's life is saved by his neighbor Winry and her grandmother, who are artificers of "automail" -- bionic limbs, essentially -- who accept everything the two boys own in payment to give Edward automail limbs.
The two brothers go through many adventures, all revolving around alchemy, after Edward discovers he can now perform alchemy without a "circle" (forming one instead with his body) and uses that ability to become the youngest ever State Alchemist.
There are a number of scenes in which Edward is seen defending a woman, and there's a strong tension of unresolved romance between him and Winry throughout the story.