Scryed (2001)

Blurb:
Kazuma, an Alter who uses his powers for mercenary work and the occasional heist, keeps himself out of the spotlight, providing for himself and his ward, Kanami, in the wastelands of the Lost Grounds, away from the fledgling cities that have begun to sprout from the ruins of the former Yokohama. But when he crosses paths with one of the most fervent officers of HOLY, Ryohu - an Alter himself who has decided to help bring other Alters into HOLY under the auspices of order and justice - Kazuma becomes enraged with the organization’s self-righteous attitude. He has no love for Alters that sadistically abuse their powers, but he also feels that HOLY has overstepped its authority. As he witnesses greater abuses by this special police force - not the least of which include the execution of a little girl who is discovered to have Alter abilities and the rampage of a renegade HOLY officer named George Tatsunami who has decided to take the law into his own hands - Kazuma becomes consumed with stopping HOLY. Alter-User Kazuma Torizuna may be the only one able to defy HOLY in search of the truth.

Source: www.anisearch.com/manga/1492