The Xenomorphs and Machines War is a military conflict that took place in an unknown year, probably somewhere in the 45th century, between the Xenomorph species and the machine civilization on Earth.
After the truce has been agreed on and humans, machines and exile programs coexisted without further conflicts an asteroid crashed on Earth. It was later discovered that this was actually a spaceship in disguise. On this ship were an Engineer and two Ovomorphs. The Engineer died shortly after coming into contact with the toxic air of the post-apocalyptic Earth, furthermore his body was dissolved rapidly.
It is unknown how the eggs reached Zion nevertheless they did. One of the alien eggs contained a Royal Facehugger and led to the birth of a Queen. Most of the population of Zion was infected shortly after the Queen had fully evolved. The persons in charge were completely overstrained and did not know how to react properly.
In a short span of time the central regions of Zion were populated by a large amount of Xenomorphs controlled by a Queen which should later be known as Zion´s First Queen. Only a few humans could escape the doomed city before the Xenomorphs took full control over the city. The last regions that fell were the outer regions like the hangar bays et cetera.
The human survivors begged the Machines to help them however, the machines did not acknowledged the Aliens as a possible threat to them. They dismissed any help and only stationed some Guardians near the infected city to prevent Xenomorphs from entering the cities of the Machine civilization.
Only after a few Xenomorphs were able to infiltrate the machines cities and sabotage a lot of facilities the machines began to act. The mainframes of the machines had only theoretical knowledge about Xenomorphs, because of the last infestation being thousands of years ago even before the war of machines and humans. The Deus Ex Machina proposed sending a gigantic army of Guardians into the Hive to destroy it however, his plan failed and the Guardians were defeated by the alien invaders.