Well, first of all, Jiraiya might return in some form, like a spirit guide or something, and be an ally to Naruto. Tsunade would also be there, using her leadership and medical ninjutsu. And then there are the new generation characters like Boruto. He could learn from Naruto and help out, seeing as he also has his own unique abilities. The Allied Shinobi Forces from the previous big battles might also reunite to support Naruto in saving the world.
Sakura and Sasuke are very likely allies. Sakura has her medical skills and combat abilities, and Sasuke, despite his past issues, has great power. They've been comrades with Naruto for a long time.
Sakura would definitely be one of his allies. She's always been by Naruto's side, and in this fanfiction, she could help him with his disguises, like using her medical ninjutsu to create more realistic physical changes. Kakashi could also be an ally. His intelligence and experience would be valuable in planning Naruto's undercover missions. He could teach Naruto how to act more convincingly in different disguises.
I think Gaara could be an ally. Gaara has control over sand and is very powerful. He and Naruto have a mutual respect for each other. Additionally, Jiraiya. Jiraiya was Naruto's mentor and has a vast knowledge of different jutsu and combat techniques that could be used against Omega Shenron.
Sasuke would be a likely ally. They have a long - standing relationship and have fought side by side before. Sasuke's Sharingan and his own unique abilities would be a great asset against the Ten - Tails.
I think Hinata could be an ally. She has always been in love with Naruto and would not stand by while he is in danger from Dark Naruto. Additionally, Shikamaru is smart and strategic. He might see the threat of Dark Naruto to the village and decide to assist Naruto, using his intelligence to come up with battle plans.
Sakura could also be an ally. As a medic - ninja, she could help Kagome if she gets injured. And Sakura is used to dealing with strange situations and new people, so she would be open to helping Kagome.
One unlikely ally could be Zetsu. Zetsu is usually seen as a villain, but in a fanfic, he could have his own motives for helping Naruto defeat Pain. Maybe he wants to disrupt the Akatsuki's plans from the inside and sees Naruto as a useful tool for that.
In some fanfictions, Orochimaru might be an ally. He has always been interested in Naruto's power and could see an opportunity in Dark Naruto. Another could be Sasuke. If Sasuke is still on his revenge path and sees Dark Naruto as a way to bring down the village, he might team up. And there are also some fan theories that some of the outcast ninja from Konoha who have grudges might side with Dark Naruto.
There could be some of the older Uzushiogakure ninjas who survived the previous disasters. They would play an important role in guiding Naruto about the secrets of the village. And maybe some new characters could be introduced, like a young Uzushiogakure ninja who looks up to Naruto and helps him in his quest to save the village.
Kakashi could still be an important ally even though Naruto has become a Jounin. Kakashi has a wealth of experience and knowledge that Naruto could still learn from. He could offer advice and assistance when Naruto faces tough challenges in his new role.