In the first manga pilot, Naruto was actually a demon fox and lived his life as a human boy as well as the Nine-Tailed Fox that attacked the village was his father.
Later during the anime, Crew twenty five and Sasuke have been sent to research the information extracted with the captured Shojoji about Kara's existence in Amegakure. Upon their return, they figured out that Kara had way back abandoned their facility in Amegakure and ended up doing Organic experiments.
Naruto then invited Boruto to eat with him at Ramen Ichiraku to test to bond with him wherein he recognized. Since they ate, Naruto explained to his son about many of site the important Reminiscences he experienced from the store, for example currently being acknowledged by Iruka, hanging out with Crew 7, and happening his initial date with Hinata.