It’s one of the Infinite or Crisis issues. Superboy Prime already got his ass kicked, and is in the future at a museum where he is reminded of that battle, which is ancient history. He finds his solar suit and proceeds to throw the superboy special tantrum laying waste to everyone and everything around. There’s an intergalactic prison mentioned as well, and I believe if memory serves, at the end, the original Superboy is revived, after being in stasis for a few hundred years to recover after he fought prime.
Final Crisis: Legion Of Three Worlds comes to mind. I could be wrong.
Connor/Superboy does return in Legion of 3 Worlds. Does the story you are looking for involve the Time Trapper as villain?
How many times has Conner dies post IC?