Just when he overtook Sasuke in their last jutsu clash Naruto was blindsided by a sneak attack from behind, but instead of killing him, Kabuto knocked him out. Seeing this as a golden opportunity Kabuto proceeded to bring Naruto over to Orochimaru as some sort of twisted present. A stunned Orochimaru initially was wary of keeping Naruto around due to the threat of Akatsuki looming over his shoulder, as well as that perverted oaf of a teammate would no doubt do everything in his power to rescue his precious pupil's son... but it would be foolish to discard such a unique test subject that guaranteed to produce interesting results.
Gleefully Orochimaru with the help of Kabuto started a long sequence of non-stop experiments on the poor boy for the next two months. During this time Orochimaru made many breakthroughs in his research and through many blood samples and siphoning the kyubi's chakra Orochimaru was able to create a medicine to partially heal the damage his blasted sensei did to his arms. Just as Orochimaru was about to siphon more chakra from the unconscious blond in a poof of smoke a small purple snake appeared, coiling around his arm it spat out a scroll.
Glancing at the contents Orochimaru tsked in annoyance.
"Well, sadly our time together has come to an end...however, before we depart let's try one last experiment." Orochimaru grinned maliciously, "Kabuto, Naruto-kun here is a prime candidate to test the Chimera jutsu. Bring one of the disposable Uchiha clones." Orochimaru ordered, starting to draw the required seals on Naruto's stomach, "but first order Guren to transport Sasuke over to our base in Iwa." Doing as he was told Kabuto informed Guren of her mission and he quickly came back with a lifeless genetic clone of one Mikoto Uchiha. Placing the body on top of the boy Kabuto performed the handsigns for the Chimera Jutsu, causing the seal on Naruto's stomach to light up.
"AAAAAAAHHHHHHH!"
Naruto screamed in agony, his body convulsing violently as the clone's body slowly absorbed into the seal.
"BOOOOOOMM!"
A pillar of red chakra exploded out from his body destroying a good chunk of the base, sadly however Orochimaru erected a defensive wall in time to protect himself and Kabuto, coming out completely unharmed. The two stared on in curiosity as Naruto's body was enveloped in a dense cacoon of chakra.
"NARUTO!"
A huge toad crashed down in between Naruto and Orochimaru, with a pissed-off Jiraiya jumping off its head and Smashing Orochimaru into the ground with a rasengan... only for his body to turn into a pile of mud. The real Orochimaru appeared a distance away laughing mockingly at him.
"Kukuku, while it's nice seeing you again I believe it's time to take my leave. Do take care of Naruto-kun for me, he has been a splendid guest and I can't wait to see how he turns out," spoke Orochimaru with a chuckle, vanishing in a plume of smoke along with Kabuto.
As much as Jiraiya wanted to hunt down that snake bastard and teach him a lesson Naruto's safety was his top priority.
Turning his attention back to Naruto, Jiraiya prepared a sealing tag to suppress the kyuubi's chakra only for the chakra to dissipate right as he was about to apply it. "W-WHAT THE HELL!" He freaked out at the sight before him, Naruto's appearance drastically changed by one of Orochimaru's vile experiments. "D-Don't worry kid, Tsunade can fix this!" He said to the unconscious Naruto.
Scooping Naruto up in his arms Jiraiya hopped back on the toad and ordered it to go full speed towards Konoha.