The Assassin and His Cygnet

Shun "Andromeda" Fujisawa may look quite innocent and timid, but he is the most dangerous assassin for the order of Sanctuary.

Prince Hyoga, known amongst the royal court as the little "cygnet", is the second son of the Russian tsar. But he was still forced to be "princely" and proper just like his older brother, Isaak.
After the war, the cygnet went missing.
His body was never found.

That was four years ago. Now, 18-year old Shun was given another mission of "high importance" to track down and eliminate a young man known as 'Glacier' for being a "potential threat" to the order of Sanctuary. Thanks to him and his gang, the once-great city of Nagoya is now a mess.

Shun does as told, disguised as an innocent Japanese moving into the area. He would never forget his mission, but upon seeing the mysterious Glacier, he decides that this is going to be much harder than he thought. To add to that, Shun discovers some unsettling truths about the order of Sanctuary that had been covered up...

Quick notes: I own the cover art, but it's clearly not of the best quality.