Quoth the Raven "Nevermore" (FULL SUMMERY AND SPOILERS)

WARNING: This pushes the boundaries for shonen-ai and the later chapters are practically "yaoi" levels of nsfw.

SPOILERS BELOW:
So, Samuel and James are members of two separate criminal organizations: Serpanti vs Hawk. Samuel is focused on murdering the Headmaster (Rugal) of the school setting and James is to be Rugal's protector. The first chapter is dedicated mostly to the constant fighting done at school and little is known about the main plot yet.

As things get going, James realizes that Samuel is the brother of James' now dead lover Samantha and things get more interesting. Confused over the multitude of different emotions he feels, James begins to get along better with Samuel but Samuel is adamant about killing Rugal the Headmaster. Why? Because Rugal was once Samuels' lover and is a psychopathic murderer who manipulated Samuel into killing Samantha--his own sister...
Unable to come clean for his part in Samantha's death, Sam tries to help James uncover the truth about his Boss "Angel" and his connection to Rugal the Headmaster/Pin-king.

As the story goes, we are introduced to side characters like Dio and Brett (side couple and...) as well as Ricky--the prick son of Rugal and just as twisted. The plot unfolds and it turns out that a dangerous drug named "Nevermore" is being distributed. The drug itself is a basic pain reliever but it has the side-effect of making the user susceptible to mind-control/brainwashing. Using this method at separate times in the past, Rugal was able to manipulate the memories of Samuel and James both.

James in the past was an orphan saved by Angel from being used as an unwilling drug-mule (by Rugal's men) and has been devoted to Angel ever since. However at some point, Rugal sees James' in person and "falls in love/obsession" with James due to his unwavering loyalty and innocent qualities. Seeing this, Angel does his best to protect James from falling into Rugal's hands but ultimately fails. He fails because his underling sells him out to save the sight of his lover (the Bar Nest bartender who was being blinded by Rugal all so this would happen) and is shot and killed by a brainwashed James who later forgets everything. Meanwhile, Samantha and Samuel are both connected to Rugal with Samantha having saved her brother Samuel from being a drug-mule (like James) by serving Rugal. Rugal went on to take Samuel as a plaything and get him wrapped up in the underworld while Samantha was sent to spy on James/Angel prior to Angel's death. She realized how dangerous Rugal is and tried to warn Samuel but he unwittingly told Rugal (as they are lovers at the time) what Samantha said and Rugal then tricked Samuel into snipe-killing his sister.

Due to all these events, Rugal has been in control of both underworld organizations and had purposely set up things so James would be with him everyday as his "protector", having used James' blind faith in his order from "Angel" to commit acts he never would...basically while Angel never had James do evil when he was alive, Rugal gave out orders as Angel (since he killed Angel through James and conspired with Angel's subordinate) that James blindly followed despite being horrible acts because James was so sure it was for a greater good...safe to say, when James learns all this he's about to go batshit crazy...but doesn't because Samuel is right there with him losing his mind too. Together, the two of them overcome Rugal and officially get-together.

1 Year Later and SamuelxJames are going strong. Bartender and his traitor of a lover are going strong (and Bartender gets his eyesight back). And DioxBrett (who would require a whole 'nother summery) get together officially since Dio is now in college and Brett has promised to quit doing illegal things (He-as it turns out-is the leader of the Serpanti organization that Samuel was a part of).

The whole thing ends with RUGAL COMING OUT OF NOWHERE--RAPING JAMES WHILE TAUNTING SAMUEL ABOUT IT--AND THEN F*CKING DISSAPEARING! (granted, he swore he'd never bother James/Samuel again but omfg--why would the author need to add this!?) All in all a great read ~

SPOILERS END