Thanos is extremely powerful with the Infinity Stones. However, Tony Stark has a history of coming up with solutions against seemingly unbeatable odds. In a fanfiction, the author might give Stark an edge by having him discover a hidden weakness of Thanos or develop a new weapon that can neutralize the Stones' power. So, it's possible for Stark to win if the story is written in a way that emphasizes his ingenuity.
Thanos could also win in a fanfiction. He has incredible strength and the power of the Infinity Stones at his disposal. In a lot of fanfictions, the power levels are often exaggerated. Thanos could simply use the Reality Stone to make Iron Man's weapons ineffective or use the Time Stone to freeze Iron Man in time and then defeat him. His brute strength alone is enough to overpower Iron Man in a direct confrontation. And his experience in battles across the universe gives him an advantage over Iron Man who mainly operates on Earth.
Naruto would likely win. Godlike Naruto implies he has extraordinary powers. Naruto has strong chakra reserves, and his signature jutsus like Rasengan are extremely powerful. Also, his ability to quickly adapt in battle gives him an edge over Orochimaru.
One interesting scenario could be Tony Stark using his superior intellect to outwit Thanos in a battle of wits rather than just brute force. He might create a device that can nullify the power of the Infinity Stones for a short time.
One group that could be the kidnappers are AIM (Advanced Idea Mechanics). They're always interested in getting their hands on advanced technology, and Stark has plenty of that. The Ten Rings terrorist organization is also a possibility. They've targeted Stark before and kidnapping him again would be a way to make a big statement. And let's not forget some rogue elements within S.H.I.E.L.D. who might think that Stark is a threat and kidnap him to keep him in check.
Pepper would be a likely candidate. She has a close relationship with Tony already, so she'd probably step up and take care of him. She has experience dealing with Tony's antics, so she could handle baby Tony's needs too.
It's hard to say. Naruto has his powerful Nine - Tails Chakra and Sage Mode. But the five kages are also very strong. However, Naruto has a habit of coming out on top in tough situations, so he might be the likely winner.
It really depends on the context. If it's a physical fight based on brute strength, Naruto would likely have the upper hand. He has access to the Nine - Tails' chakra which gives him superhuman strength. But if it's a fight that involves strategy and medical ninjutsu, Sakura could potentially win. She's a very intelligent fighter and her medical skills could be used in a creative way to disable Naruto.
Probably the other Avengers like Captain America. He could play a role in trying to save Tony or in the fight against Thanos that ultimately leads to Tony's death. Maybe Doctor Strange as well. Since he has knowledge of the future and the Infinity Stones, he might be involved in some way. He could either try to prevent Tony's death or his actions could inadvertently lead to it.
It depends on how the OC is designed. If the OC has super - powerful and rare Pokemon, it might have an edge. But Alain is a very experienced trainer, so he could also win with his battle smarts.
In a straight - up fight, Batman might seem more likely to win. He has more experience and a wider range of skills. He has trained Nightwing, so he knows his fighting style well. However, Nightwing is younger and more agile, which could give him an edge in a fast - paced battle.