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Aether is a pressurized substance that fills the space of the magic universe. It is the property of that space that allows magic to exist. The physical (sci-fi) universe has no aether.
The magic universe is an alternate physics engine. It has similar fundamental particles and similar fundamental forces to the physical universe. All the particles in the magic universe are collectively called magical carrier particles.
Gravity and the strong force roughly work the same way in both universes.
There are slight differences that lead to interesting consequences. For example, there may be no relativity in the magical universe, while there is in the physical universe.
The two universes haven’t diverged so much that magical particles and physical particles can’t interact. The difference is that magical particles carry magic.
Magic turns into magical carrier particles when it is transferred from one universe to the other.
Magical carrier particles decay in a vacuum with no aether. This is why magic can’t survive in the physical universe on its own.
When the two universes collide, the aether wants to spread into the rest of the universe. Aether is pressurized and the vacuum of the physical universe is empty, so by the laws of thermodynamics it leaks out.
In the sci-fi world:
Areas form where magic is allowed to exist, but only for a period of time. Then the aether disperses like water vapor.
Aether interacts poorly with the particles of the physical universe. Anything that comes into contact with aether is damaged or destroyed.
In the fantasy world:
The aether becomes thinner and thinner.
Magical carrier particles start having more and more malfunctions.
In some places magic stops working altogether. This has cultural consequences: religions stop functioning, which can lead to societal collapse.
If the leak continues long enough, the aether content of the combined universe becomes too high for regular matter to exist and too low for magical particles to exist. The result is a state of perfect disentropy: the whole universe becomes uniformly aether and energy, and all particles are destroyed.
Preventing perfect disentropy is the central threat that the characters are trying to stop.
Because aether is a physical substance, the threat is a physical problem: how to keep a liquid from leaking out of the other universe.