In order to finance the military operation he has begun, Nick Fury sends the Secret Warriors on a mission to rob HYDRA money stored in a Swiss bank. On learning of this outrage, Baron von Strucker calls on Norman Osborn, the current head of US national security and superhuman affairs to have Nick Fury killed. Nick instructs his team to lie low, and forbids them from taking more than $20 from the pile of cash, which Hellfire strongly resents.
Cooped up at Nick Fury's base #22 Inside Straight, Hellfire and Phobos intercept an SOS message from Black Widow, whose cover as a member of the Thunderbolts has been blown. The two make plans for a rescue. In New York City at Fury base #20 Homerun underneath Yankee Stadium the fugitive Songbird and Black Widow meet Phobos disguised inside a Nick Fury Life Model Decoy. The three are ambushed by the Thunderbolts and Dark Avengers. While Songbird and Black Widow are taken away, Osborn berates 'Fury' before shooting him in the head, only for Phobos to reveal himself inside the decoy. Watching from outside, Eden Fesi and Hellfire break in, disguising themselves as HAMMER agents, and they spring Phobos from Osborn's clutches with the help of Ares who wants Phobos to be given a fair chance to escape. The three heroes escape to the roof, but as Eden teleports back to Inside Straight, he fails to stop the Dark Avengers from following through, and the self destruct sequence is initiated. The rest of the Secret Warriors, including a recovering Yo-Yo and a huge number of Nick Fury LMDs battle the Dark Avengers and escape back to Fury base #17, The Cocoon while the base explodes.
Nick Fury meanwhile goes to Toronto, Canada where he recruits former SHIELD agent John Garrett. The two track down US Treasury staffer Seth Waters, who they suspect of being a spy, possibly for HYDRA. Garrett meets Waters in his office in Washington DC, where Seth reveals that he knows Garrett was Aquarius: a member of the original Zodiac twelve from the Pieta incident. Later at night in New York City, Fury breaks into Stark Tower with the help of Garrett, and he goes to meet Osborn. Fury tells Osborn about Seth Waters and has Osborn bring him in for questioning. After being tortured by Bullseye, Waters gives up a name ' Leviathan,' at which point John Garrett shoots a massively powerful rifle through the building walls, killing Waters. Fury escapes with the data chip belonging to Waters to base #7 Pieta, where he learns that Leviathan is the Russian rival spy organization, formed to counter HYDRA and SHIELD.
In flashback, we learn that in ancient history, Phobos had killed his father Ares with a powerful sword called Grasscutter during a war between the Gods. Later, Ares entrusts Phobos to Nick Fury's teaching and care, before bringing him before the assembled Gods of Earth's many pantheons, where he is named God of Fear. Ares tells him he will not become a true God until he dies and is reborn.
This story arc is significant for bringing into play a third, global secret organization: Leviathan, begun by the Russian leaders Magadan and Orion in response to SHIELD and HYDRA.