The basic idea here is that both the Negative Zone and the Phantom Zone are one and the same.
The story that I had thought about using with the above idea is a 3 story arc.
1. A Kryptonian supervillain escapes into the Marvel Universe and starts to wreak havok. The heroes have to unite in order to stop him. It ends with the heroes realizing that the villain came to their world via the Negative Zone and decide to take an expedition.
2. The Marvel Heroes come upon with the emprisoned Kryptonians who convince the heroes that they were wrongfully put there by a malicious dictator. The heroes, not sure of what to do, decide to help the Kryptonians, even going against the advice of a few of the inmates. When they arrive in the DC Universe, they get into a figh with whomever happens to be at the Fortress of Solitude, and end up gaining the upperhand long enough for one of the Marvel heroes to turn n the Phantom Zone Project allowing the Kryptonians to go free. It is only then that the Marvel heroes realize that they were duped.
3. The Marvel and DC superheroes team up to capture the escaped Kryptonians.
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