Scorpia by Anthony Horowitz

Scorpia is a secret organization that stands for Sabotage, Corruption Intelligence and Assassination. Alex decides to go to Venice. When he arrives he finds head quarters in a building. When he enters Nile, another assassin finds him and puts him in a close room to drown. Alex manages to escape and tells Nile who he is. Nile understands he is John's son and doesn't kill him. Alex decides to start working for Scorpia. Scorpia has a plan: kill all children aged 12 through 13. This plan is called Invisible Sword. They send alex to kill a person. When he shoots to the person, he is caught by MI6 and later finds out that the person he had to kill had a bullet-proof jacket. MI6 sends him back to Scorpia to find out more on their plan, and he stops them. When he returns to MI6 a scorpia's assassin shoots him. The story ends with him being apparently dead.