Maybe the gate is a portal to a world where the ninja arts are completely different. Naruto teams up with local ninjas there to stop an evil force that threatens both worlds. For example, they might have powers based on elements not seen in the Naruto world, like crystal or sound manipulation at a much more advanced level.
A cool plot could be that the gate is a time - traveling portal. Naruto goes back in time and meets the founders of the Hidden Villages. He has to use his knowledge from the future to prevent a great disaster that could change the course of ninja history.
One interesting plot idea could be that the characters from Anime Gate end up in the Naruto universe during a major ninja war. They could use their unique abilities from their own world to help turn the tide of the battle. For example, if there are characters with special time - controlling powers in Anime Gate, they might be able to stop a powerful jutsu from being launched at the last second.
One idea could be Naruto being transported to the Gate Jietai world and having to learn their combat techniques. He might use his shadow clone jutsu in unique ways during battles there.
Maybe there's a plot where a powerful and rare Pokemon is causing chaos in the Naruto world. The Naruto characters have to team up with some expert Pokemon trainers from the Pokemon world to stop it. Naruto could learn about the unique bond between trainers and Pokemon and apply some of those concepts to his relationships with his friends. And the Pokemon trainers could be in awe of the ninja techniques and use some of that knowledge to improve their own strategies.
A possible plot is that the Zoids themselves gain some of the abilities of Naruto characters. Imagine a Zoid being able to use chakra and perform ninjutsu. A Fire - type Zoid could use the Fireball Jutsu. This would completely change the dynamics of Zoids battles. Also, the story could revolve around a group of Naruto characters trying to stop an evil force in the Zoids world that is using Zoids in a way that could destroy both the Zoids world and the Naruto world. They would have to learn about Zoids and team up with local Zoid pilots to fight against this common enemy.
One idea could be a character from Naruto ending up in the Descendants' world. For example, Naruto himself could be transported there. He might use his ninja skills to deal with the challenges in the Descendants' world, like facing off against the villains in a very different way compared to the Descendants' characters. Maybe he'd use his shadow clone jutsu to confuse the bad guys or his Rasengan to take on powerful foes.
One idea could be that members of Root are sent to infiltrate the Hidden Leaf under the guise of being friendly shinobi. They cross paths with Naruto and his friends. Naruto, being the perceptive one, senses something off about them. This could lead to a series of battles and mind games as Naruto tries to expose their true motives.
Maybe there's a crossover where the Kyuubi's chakra has some strange effect on the Gargoyles. It could either enhance their powers in unexpected ways or cause some sort of chaos that they have to work together to fix. For example, the Kyuubi's chakra might accidentally awaken an ancient evil in the Gargoyles' world, and Naruto and the gargoyles must use their combined strength and wits to stop it.
Maybe in this crossover, Naruto has a vision of the Traveler from Destiny. Curious, he somehow manages to cross over to the Destiny universe. There, he meets the different classes of Guardians. He could learn about their weaponry and powers and in turn, teach them about chakra. They could then work together to stop a Vex invasion that is spreading across both universes.
One idea could be that the countries from Hetalia are somehow transported into the Naruto world. For example, Italy could end up in Konoha and his carefree attitude might amuse or annoy the ninja there. Maybe he gets involved in a mission by accident and his unique skills from being a nation, like his knowledge of different cultures and languages, could come in handy. Another plot could involve Naruto being sent to the Hetalia world and having to deal with international relations in a very different way than he's used to in the ninja world. He might try to use his ninja way to promote peace between the nations there.
Another plot could involve Obito being reborn in Naruto's world at a different time. He has no memory of his past life initially. Naruto meets him and they become friends. As Obito starts to regain his memories, he has to decide whether to continue on the path of his previous self or to embrace the new relationships he has formed with Naruto and the others. It could lead to a great internal struggle within Obito.