Daikenja Riddle no Jikan Gyakkou

A young man named Riddle had lost all of his friends—and the entire world—at the hands of a mysterious organization known as the "Box of Malice." Having lost all hope to live, he dwelled in a pit of despair until he has one final revelation. What if... he could return to a time before everything ended? And so, after a thousand years, a deformed Riddle finally manages to reverse time. "I'm going to stop them this time...!" Equipped with a thousand years of knowledge and experience in his young body, the Great Sage Riddle's journey to the past now unfolds!

(Source: Shogakukan, translated)