One idea could be that Team Konohamaru travels back to the time of the First Hokage. They could witness the founding of Konoha and get involved in some of the early battles against rival clans. Maybe they help Hashirama in some way and learn valuable lessons about leadership and unity from him.
Another plot could be that they travel to a future where Konoha is in ruins. They then have to figure out what went wrong and try to change the course of events in their own time to prevent this dark future. Along the way, they meet older versions of their friends and family who are different due to the hardships of this post - apocalyptic Konoha.
In a team Iron Man time travel fanfiction, a great plot could be that Iron Man travels to the future by accident. There, he discovers a world in ruins because of some actions he took in his present. So, he has to travel back and correct those actions. He teams up with his past self and other Avengers from different time periods to make sure the future is saved. This would involve a lot of character development as the different versions of Iron Man and the Avengers have to work together and understand each other's perspectives.
Maybe they time travel to a point where a major battle was lost in the past. Kakashi and Team 7 could change the outcome of that battle. For example, if they go back to the battle against the Nine - Tailed Fox when it first attacked Konoha. They might be able to prevent some of the destruction and save more lives. Or they could travel to a time when a powerful ninja was wrongly exiled, and they work to clear that ninja's name and change the course of history.
Perhaps they travel to a time in the past where a powerful and dangerous jutsu was first created. They have to stop the jutsu from being misused in the future. Along the way, they face challenges like dealing with the original creator who might not want to give up on his creation, and also face other ninja who want to steal the jutsu for their own evil purposes.
They could travel to the past and accidentally change something that has a huge impact on the present. For example, Naruto might prevent an event that was crucial for the development of a certain jutsu. This would then lead to a series of challenges as they try to fix the timeline.
One idea could be a story where Konohamaru is kidnapped and Naruto has to use all his skills to rescue him. It could show Naruto's growth as a protector.
Another plot could be that they go back to a time when a great ninja war was about to start. Team 7 could try to prevent the war by changing certain key events or by uniting the warring factions. They might use their skills and knowledge from their own time to broker peace deals and stop the bloodshed before it begins.
Definitely Naruto. Even if it's a Team Konohamaru time travel fanfiction, Naruto's presence can add a lot of excitement. He could offer his unique perspective and skills, and his interactions with Konohamaru and the team would be really interesting, especially if they travel to a time when Naruto was younger or not even born yet.
One idea could be Yoda traveling back in time to train Anakin Skywalker differently, thus preventing his fall to the dark side. Maybe he goes back to the very beginning of the Jedi Order to gain more knowledge about the Force and bring it back to his own time.
One idea could be Shinji traveling back in time to prevent the Second Impact. He might try to change the actions of his father that led to it. Another could be Asuka traveling to a future where the Evangelions have been completely forgotten and she has to figure out how to get back to her own time.
Another plot could be a character from the future coming back to the present in Shameless. They could be trying to stop a future disaster that is somehow linked to the Gallagher family. This would involve a lot of mystery and intrigue as they try to figure out what the future event is and how to prevent it while dealing with the chaos of the present - day Gallagher family.