Plot Summary

Nick Fury, suspicious of the current state of affairs after the dismantling of SHIELD, following the end of the Skrull Secret Invasion, breaks into The Carousel, a SHIELD base in Chicago. This information leads him to send the Secret Warriors to recon the Black Ice facility in Odessa, TX, where they break cover and battle both HAMMER and HYDRA forces. HYDRA manage to escape and steal a casket containing the remains of the Gorgon. The fact that HYDRA showed up prompts Fury to announce to his team that SHIELD was evidently working under the control of HYDRA all along.
Meanwhile, in the Ichor HYDRA base, an attack by Skrulls leads Baron von Strucker to destroy the base and regroup the leadership of HYDRA: Kraken (actually Jake Fury), Viper, Madame Hydra (actually the Contessa) and The Hive. HYDRA then bring the remains of Gorgon to the Hand where they force the assassin clan to revive Gorgon, taking the life of the Hand Grandmaster in the process.
The Secret Warriors are next sent to evacuate some psi-agents from the Red Worm SHIELD base but are again confronted by HYDRA. Gorgon cuts off Slingshot's arms during the fight and HYDRA leave with the captive agents. The Secret Warriors seek out a replacement for Yo-Yo and find Eden Fesi - a teleporter living in Australia. Fury goes to the Sudan to recruit the former Howling Commandos soldiers. He assembles an army that attacks The Dock - a SHIELD base under HAMMER control. During the battle with HAMMER, HYDRA forces again show up, and the Secret Warriors are called to the rescue, allowing Fury to get away with three helicarriers.
Following this event, Madame Hydra and Viper bargain with the Silver Samurai and obtain a mysterious box from Clan Yashida. Kraken orders HYDRA to scan all members for a traitor in their ranks. Fury instructs Dum Dum to start recruiting an army. He reveals to the Secret Warriors that he was not the one who called for their aid in the battle.

This story arc set the scene for the Secret Warriors series. It turned Nick Fury's world view apparently on its head by showing that HYDRA had secretly had control over SHIELD for many, many years.