The Avengers are in the mansion discussing their recent defeat at the hands of Arsenal. Hawkeye is tired of being a "temporary Avenger" and stalks out of the meeting thinking he'll get a quick workout in the gym. The Beast follows him and Hawkeye starts jumping at shadows and fires an arrow at the Beast! Beast catches it in his paws and Hawkeye mellows. Just then, they discover a giant hole in a wall of the mansion. It leads to a subterranean cavern several levels below the mansion.
The cavern was created by Project Tomorrow whom the Avengers discover was planned by Howard Stark. Project Tomorrow created Arsenal as a last ditch defense should the Axis powers actually win World War II. He was activated by accident and started his rampage still fighting the War. Also in the cavern is "Mistress", a computer imprinted with the brain patterns of Iron Man's mother Maria. Mistress is able to control Arsenal remotely and also spontaneously repairs any damage that Arsenal may incur.
The first battle has Hawkeye and the Beast surprised by Arsenal. Beast is knocked cold with one punch, and Hawkeye gets tangled up with one of his own arrows. At insect size Yellowjacket had been following Hank and Clint; Mistress spies him and tries to gas him into unconsciousness. Yellowjacket escapes and is able to warn the rest of the Assemblers that Arsenal resides below the mansion.
The battle is joined! Captain America, Thor, Iron Man, Scarlet Witch, and Wonder Man enter the cavern, while Jarvis takes care of Yellowjacket. Shortly after the team left, Vision returns from elsewhere. Hearing about the current crisis, he too heads for the caverns and thanks to his intangibility reaches the robot before the team does. He gets himself disrupted by Arsenal who somehow causes the Vision's intangible state to become unstable. In pain, he screeches off into the sky screaming.
Nearby Wanda hears him scream and is the first to take a crack at Arsenal; she is even able to do some damage! Arsenal takes two shots from her, and is staggered when he somehow manages to strike out blindly and knock out the witch. Wonder Man takes the next shot at Arsenal and is swatted down the cavern where Thor is forced to leave the battle and fly after him. Wondy is washed up in an underground river. Mistress senses that the power of Thor could defeat Arsenal, so she whips up the underground river into a maelstrom and spits Thor and Wonder Man out to sea. (The river flows through her cooling system so she controls it that way)
Cap is holding off Arsenal in the cavern and Iron Man decides that he is the one to take on Mistress. He makes the decision to leave Cap and tackle the computer. Iron Man rescues Hawkeye and Beast (they were strapped into an interrogation device) while Cap gets thrown over the side of the chasm. Cap is rescued by Thor and who is flying back up the chasm to resume the battle after he and Wonder Man found the unconscious Vision near the river.
Meanwhile, Iron Man decides to reason with Mistress by showing her his face and stating that he is her son and that Howard Stark is not returning. Mistress, realizing the truth, decides to shut down rather than go on without Stark. Once she is shut down, Arsenal is on his own and unable to regenerate himself. Thor and Scarlet Witch pour it on and Arsenal is blown up. Iron Man flies out of the cavern after the explosion and thus the battle ends.