Years ago, Vangus led the Ixions in an attempt to plunder Earth's oil, which is an extremely valuable commodity on the intergalactic market. They were stopped by Alpha, who convinced the Ixions to delay their invasion for some time. Alpha would later betray the MiB and steal the Cosmic Integrator as part of his bid to create a perfect body for himself.
Thirty years later, Vangus returns, forcing MiB to turn to Alpha (whom they have in their custody at the time) to learn how to defeat them. Alpha's information got results, but at the cost of his manipulating Jay into helping him escape and ally himself with Vangus. Jay eventually managed to thwart both of them, but Alpha escaped, though Vangus was brought in to custody, forestalling the Ixion invasion.
Alpha arranges for Vangus to escape from MiB custody and they team up together to conquer the Earth. As part of the deal of giving Vangus and the Ixions the oil, Alpha will get to rule the Earth. Vangus uses the Ixion armada to lay waste to the lands, leading to catastrophic destruction across the world, as well as seemingly incontrovertible proof of (hostile) alien life. Earth puts up a powerful resistance, and while Vangus celebrates the success of his forces, Alpha becomes impatient and destroys MiB headquarters itself.
To their disappointment, MiB lives on, and considering the dangerous threat to the world, the MiB has revealed themselves to the world in order to pull up a combined effort to strike back against the Ixions. Jay and Kay go into space to stop Vangus and Alpha, but are caught and put into a cell. In the meantime, however, Vangus becomes even more impatient, since he expected destroying MiB headquarters to bring "instant victory". Vangus decides to cut their losses, destroy Earth itself with a powerful missile, and reap its oil later, despite Alpha's objections that that will leave him no populace to rule. Vangus turns Alpha's metaphor of "You can't make an omelette without breaking a few eggs" against him, which does nothing to convince him, and a fight breaks out. Vangus knocks off one of Alpha's cannon arms, which slides over to Jay. Jay uses it to shoot both Vangus and Alpha. Vangus is stunned, but recovers long enough to set a missile to destroy Earth and escape, claiming that he will be back to "clean up the mess". Despite having escaped, however, Earth is saved as Jay and Kay manage to destroy the missile with Alpha on-board, much to Vangus' dismay.