The fourth was on a spy mission in ther hidden village of rain when he met up with a female rain ninja, he used some sort of genjitsu and seduces her but he didnt know that this female ninja has had more turns than a door knob and contracts Herpes. Unknowingly to his knowledge Pein is born 9 months later (piercings and all, lol)
A few years later when he ask Tsunade before she leaves the village to cure him of Herpes she does and to retunr the favor he sleeps with her. She becomes pregnant and she doesnt want anyone to know and leaves the village to give birth with Shizune at that time 9 months later Naruto is born. (Yes, Tsunade is Naruto's mother)
A few months later, Naruto shows up in a basket at the village orphanage with a name tag that said Uzumaki Naruto, please take care of me. The fourth realizes who this kid is and is seriously worries that people might find out in the village.
Unfortuantly, the Kyuubi attacks the village and the fourth goes and fights but realizes he is not strong enough so he picks Naruto to harbor the Kyuubi because he is the only kid available at the orphange at the moment.
Naruto and Sakura will find out about all this when they get married which happens to be the day Tsunade dies and does not want to die with a guilty conscience.