After the fiasco that was Harry Potter's 5th Year at Hogwarts Harry was forced to take Occlumency lessons from Severus Snape. Severus had seen what Sirius's death did to Harry and lessened his torment of the young Gryffindor. In time they became friends and eventually fell in love with each other. They kept their love a secret until they could be sure it was safe for them to come out and Voldemort was dead.
The final battle happened and Harry won but was badly injured. Poppy Pomphrey healed him and found out that he was expecting a baby. Harry was ecstatic and went to tell Severus. However, whilst Harry was recovering Remus went to Severus with his furious realisation that the Slytherin was with Harry. The two were arguing in the dungeon corridor when Harry overheard them.Flashback
"I want you to stay away from Harry! He obviously loves you but I doubt you even know the meaning of the word love! If you don't stay away from him I'll make sure he knows precisely what you truly are!" Severus was shocked and scared of Remus's threat so did the only thing he could think to do. He decided to fob Remus off with something and then make sure that he told Harry everything before Remus could however, he didn't realise that at just that moment Harry had turned into the Potions corridor.
"You're right Lupin! I don't love him! I'm just using him! Do you want some more? Okay then, I don't love Harry Potter!" Severus cried and Harry broke into tears before running down the hall in the direction of the infirmary.End Flashback
Harry was devastated and knew that he had to go away to have the child. He could never let a child grow up like he had in a loveless environment so did the only thing he could do and ran away. Poppy Pomphrey was the only one to know where Harry had gone and became Harry's son's, Matthew Severus Potter-Snape, godmother. Harry trained his son in all branches of magic to as high a competency as an 11 year old could be when they went to Hogwarts. Harry also trained his son in wandless magic in order to ensure that the child would be able to protect himself if it became necessary.