It's a redemption story of sorts, not religious thou lol.
The story is The ICA (International Contract Agency) whom Agent 47 works for has genetically-engineered another assassin, a young girl, named Victoria, whom 47 has to protect from suffering the same path he did after his trusted handler Diana takes the girl and runs away. 47 is sent to kill Diana and retrieve the girl by the new boss of ICA. He shoots Diana but he promises Diana to keep the girl safe. He then takes the girl to an orphanage while he goes to figure out what's going on.
Long story short, there a is bad guy named Dexter who steals the girl to sell to the highest bidder, then Hitman 47 goes after him to get the girl and in the process kills everyone in his way, while the cops are chasing after him because Dexter framed him for a murder.
47 didn't actually kill Diana and returns the girl to her, Then goes to take down all the bad guys of the ICA and everyone lived happily ever after, with Diana coming back to the ICA and Hitman continung to assasinate people.
The story is not bad, but the game play takes a big hit, because you have to sneak around the whole game hiding from essentially everyone and disguises don't really do much to hide you