In case you weren't paying attention, they did explain.
The movie is just ok. It had nothing to do with the game's plot except the title character, Agent 47, which is quite a shame since the game reveals more about the Organization and a better plot as to why they betrayed him. This show is kinda cliched with the "master assasin" who everyone wants to kill but he is always 2 steps ahead, the cop that has a unhealthy obsession in catching the guy, and the beautiful girl caught in the whole mess. Yeah...sorta like Bourne movies.
Agent 47 is supposed to be a professional silent killer but in the movie he was depicted like some kinda Chow Yun Fat one against many guy. Hell they even thew in other bald guys to fight him. Oh gee....how clandestine of the super secret organization.