The Matrix vs Marvel
As a means to end to prevent the glitch of the One, Neo is killed and the Architect congratulates Smith on a job well done. The Machine god engineered the so called Smith virus to cleanse the Matrix of the Neo cycle and destroy Zion.
With Zion destroyed, the Machines seek to spread through solar systems and galaxies like a plague. Eventually, all worlds in their universe have fallen, and now they seek other universes and dimensions to conquer.
Their primary weapon is Smith, who can now replicate himself outside the Matrix. He replicates the inhabitants of worlds which leads to no resistance when they voluntarily place themselves in hibernation chambers and become jacked into the Matrix, with no recollection of previous events. With this method, the entire universe fell to the Machines.
Now, Smith has invaded Marvel Earth and already copied himself to most inhabitants of Africa, South America, and many other third world countries. Smith then opens a portal which allows millions of Sentinels into this realm to conquer the resistance and allow Smith to replicate the population of the world powers.
The Avengers, X-Men, Fantastic Four, Spiderman, Daredevil, Transformers, heroes and villains together that have appeared in the Marvel Cinematic Universe will unite against this threat. Only exceptions are Galactus, Odin, and Mephisto(Ghost Rider).
If the machines conquer Earth, Asgard is next...and Odin has already pointed the bi- frost at Midgard to destroy the threat if all else fails.
How does this war play out?
Smith has same powers as he did at end of third Matrix film.