In my Third Pulse WIP the main character is that world's version of Superman only not so strong, fast, or invulnerable. His problem is he cannot die (and ge's already died a couple of times and was presumed dead a third). If there's any kind of electromagnetics around he'll eventually come back, but more powerful and slightly "different" than before.
For the first third of the book he's been relearning his abilities after a 5-year period of regaining his memories from a "mind wipe" by a superpowered psychic. In the last third of the first third of the book he confronts his old arch enemy in Golden Gate Park, confident he can handle everything they throw at him. He sends an old partner for help and proceeds to mop the floor with his enemy's army.
So, the problem was, how to keep this guy up a tree and keep throwing rocks at him. The enemy knows he can't literally be stopped permanently. If they kill him he's only going to come back stronger and "different" and they might not be able to handle the new version, army if superpowered individuals or not.
Be he's the good guys general. They have to take him down.
Up to this point the character has also heavily overshadowed the other characters in the book. We know virtually nothing about them.
The solution?
The villains gang up on him and beat him to within an inch of his life - but don't kill him. He's captured, defeated, and in his arch-enemy's hands. His allies are leaderless, lost.
The next third of the book will be about those sidekick characters growing and becoming leaders in their own right in their attempts to rescue their leader and build their own army to oppose the enemy who seems virtually unstoppable without their Superman.
After the second third of the book the going will really get tough.