Mindbender Beginning

Hello everyone and here's another new story called Naruto: Rise of Cobra. It's idea given to me by Haseo55. I hope you like it.

Disclaimers: I don't own GI JOE or Naruto, Hasbro and Masashi Kishimoto owns them.

Valley of the end

Naruto and Sasuke lay where they are completely beaten, exhausted and battered. Before all this Sasuke was going to Orochimaru for power so he could get his revenge on Itachi. Sasuke was ignoring the fact that Orochimaru wants his sharingan, Naruto and his team went after him but they got cornered by the sound four. Shikamaru and the others manage to defeat them while Naruto deals with Sasuke.

"Kakashi Sensei help me up", Naruto said after Kakashi arrived.

"I'm sorry Naruto but Sasuke needs more help than you", what Kakashi said made Naruto go wide eye.

Naruto then screams to his Sensei as he picks Sasuke up and abandons him to his fate. Naruto still lying where he is unable to get up is now confronted by Orochimaru and Kabuto.

XXX

Orochimaru's lair one week later

Screams of pain can be heard from outside the lair, Naruto is being tortured by Orochimaru who is using a snake like whip.

"You terribly and horribly scarred him Lord Orochimaru", Kabuto said with a smirk on his face.

"I know but even he escapes he will lived with those scars for the rest of his life", he said as he continue to torture him.

XXX

1 year later Naruto manage escape his captivity and leave the Elemental Nations.

"I can't go back to Konoha not after what Kakashi did, especially not on my condition."

As the boat sails out of the Elemental Nation Naruto blacks out because he had to drag his way to a boat and get it ready to sail.

5 days and 4 nights later Naruto finds himself in some kind of lab. He looks around and sees an old man in in a video player that was recorded.

"This will only hurt a little what comes next more so", the old man ejects something into a man strap to chair.

Soon after the injection the man's skin and flesh starts to melt or get eaten away, Naruto looks at the things that were injected into the man.

"Nanomites", Naruto said while holding a sample of the Nanomites.

Naruto then sees the name of the old man, it's Doctor Mindbender.

"Magnificent isn't", Naruto turns around and sees Mindbender.

"I brought you here to see this when you recovered and I'm sure hoping you are interested on learning how to use my creation."

"Yes train me how to use them", Naruto said as Mindbender seals the door.

"I will tell you everything about the nanomites and I will give you the proper medical equipment so you can live onward", he explains to Naruto.

Dr Mindbender also gives Naruto a new ninja headband with a red cobra snake symbol on it. He even gives a mask a strange mask.

"When you're ready you can return to where you came from and start you're revenge on what they did to you."

Then a horrible laugh is heard from outside from the bunker. The one making that laugh was Naruto. It seems he is about become insane.

"Nanomites perfect little soldiers", Dr Mindbender said to Naruto.

"Nanomites perfect little healers", Naruto said next.

This chapter is finished. The story will go on like the film, Naruto will be the Doctor first before becoming Cobra Commander. First he along with Storm Shadow (same one from the film) will side with Obito/Madara Uchiha during the 4th war, Cobra will not be there until the end. The GI JOES are not there but the Shinobi Alliances are the JOES. Cobra Troopers are the same ones from the first film. Please review.

Next: Viper Commandos