The Anihilaarg first appeared in So Long, and Thanks for All the Smoothies, where a Contemelia vessel materialized in the universe and appeared above Earth, Argit was sent aboard the ship by Milleous to obtain the Anihilaarg while the Vreedle Brothers sought it for themselves.
Later in the episode, the Anihilaarg was accidentally activated when Ben, Rook, the Incurseans and the Vreedle Brothers were fighting to obtain it. It destroyed the entire universe, but Ben recreated it as Alien X. With the Anihilaarg activated, it was rendered useless.
Everyone present (other than Ben) believed that the Anihilaarg was defective, unknowing that the universe was even destroyed in the first place as Rhomboid went over and crushed the Anihilaarg underfoot, destroying it completely.
In Mud Is Thicker Than Water, it was revealed that Blukic and Driba fixed the Anihilaarg and that it was being kept at Plumber Headquarters with a fake being used as bait.
In Collect This, Ben offers a detailed replica of the Anihilaarg to Collectimus in exchange for the Earth.
In The End of an Era, set years into the future, the Anihilaarg is stolen by Subdora, Exo-Skull, and Maltruantwho combines it with energy from the Dwarf Star before fleeing on a Time Beast carriage.
In A New Dawn, Ben chases after Maltruant all the way to the beginning of the universe, who strives to replace the current one with one in his image by switching the Anihilaarg about to be used for the experiment being conducted by the Contemelia. That would result in the current universe being replaced with a different one threatening to rewrite all of its history across the branching Timestream. Taking advantage of the Omnitrix fail-safe that will keep Ben alive in the event of life-threatening conditions, Ben was able to neutralize and destroy the modified Anihilaarg and replace it with the original, creating the universe as intended.