“I can’t. If I kill her, the Philosopher’s Stone loses its power.”

Sages used the stones as a source of power. It gave them the ability to regenerate forever.

...

“Takatou... I think Sion mentioned something about you.”

“We’ve been going around fighting Sages and collecting Philosopher’s Stones. If you give us yours, we won’t have to fight. So how about it?”

“Hmm, I don’t know. You’re the one who killed Santarou, right?”

“And Lain, and Sion, and Raiza.” Though technically he hadn’t personally killed the latter two, he didn’t feel like explaining.

-Volume 9 page 149