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Origin

 Who Do You Trust?
After Nick Fury's unauthorized attack on Latveria was exposed, the one-eyed master of covert operations went underground with the belief that a conspiracy had not only infiltrated S.H.I.E.L.D. but possibly much more. His suspicions were confirmed when a Skrull posing as Contessa Valentina Allegro de la Fontaine tried to assassinate him. In order to combat this threat, he needed people he could trust, and there was no telling who the Skrulls had already replaced. What he needed were assets that no one would know about to compromise, and fortunately, he had exactly that in his list of Caterpillars. The Caterpillars were people with potentially useful superhuman abilities that he and he alone knew about. They were the illegitimate children of super villains, the unknown descendants of superheroes or randomly gifted individuals the world had not discovered yet.

 Secret Warriors
Fury's own prized agent, Quake, was the first Caterpillar he had reached out to and trained, so it only made sense that he used her to recruit and lead a new team of Caterpillars. She sought out J.T. James, the descendant of the Phantom Rider with hellfire at his command; Jerry Sledge, the illegitimate son of the Absorbing Man with the same magical power, Sebastian Druid, the son of Doctor Druid with monster blood in his veins; Yo-Yo Rodriguez, the daughter of the Griffin mutated with speed abilities; and Alexander, the son of Ares god of war. She attempts to recruit Layla Miller, but the girl informs Quake she's meant for other things and that she will become one of the greats. These Caterpillars became Nick Fury's Secret Warriors.

These were powerful but untrained and untested young people. Before they could be of any use, Fury put them through months of intensive training and explained the situation with the Skrulls.  

Creation

Secret Warriors was created by Brian Michael Bendis and Alex Maleev and debuted in Mighty Avengers #13 as a tie-in to Secret Invasion. Jonathan Hickman then inherited the team and was responsible for the large majority of its development in the self titled ongoing series Secret Warriors.

Team Evolution

Originally, the Secret Warriors were portrayed as a single small unit of superhuman operatives working directly under Nick Fury's supervision. This was shown not to be the case several issues into the ongoing series. There were, in fact, three teams of Secret Warriors operating in unison under Fury's command. The group that had been and would continue to be in the spotlight was simply Team White, but there were also Team Black and Team Gray operating in the background. 

 Team White led by Nick Fury
Team White 
Operating directly under Fury's guidance, this group was the one commonly known as the Secret Warriors. It was led by Quake and functioned as Fury's hand, doing whatever he needed doing at a given time. 
 
Team White was the focus of most of the Secret Warriors series, though the team was officially disbanded toward the end after the loss of two of its members in a major attack on a HYDRA base. 
 
Team Black led by Alexander Pierce
Team Black 
Led by Alexander Pierce, Team Black drafted the problem candidates from Fury's list of Caterpillars. Some were already in prisons and others were merely high risk individuals at the time. Unlike Team White, this group had a more defined mission, and it conducted itself outside of Nick Fury's direct supervision. Gathering intelligence on HYDRA was Team Black's objective. 
 
Team Black only appeared prominently in one arc of Secret Warriors, the Last Ride of the Howling Commandos.
 
Team Gray
Team Gray
 
Team Gray was run by Fury's son, Mikel Fury, and tasked with Leviathan much like Team Black was tasked with HYDRA. 
 
Team Gray appeared in only one issue of Secret Warriors in which the entire team died on a mission against a HYDRA stronghold. 

Major Story Arcs  

Secret Invasion

For further details: Secret Invasion
 Into the fray
The Secret Warriors were thrown into battle for the first time when the Skrulls kicked their invasion of Earth into high gear. Manhattan became a war zone with Super Skrulls devastating the city, and Fury led the team into the heart of the battle. The arrival of the Secret Warriors turned the tide of battle enough to rescue the combined forces of the Initiative and the Young Avengers from being killed by the Skrulls. Fury rallied all the other heroes together with his Secret Warriors and began a series of hit and run attacks on the Skrull forces throughout the city. But this tactic would only get them so far. It took all of them just to take out a few Super Skrulls at a time. A better chance at defeating the Skrull invasion came at the sight of Thor's lightning calling them all to Central Park. There, the Secret Warriors gathered with all of the other assembled heroes and repelled the Skrull invasion. 
 
In the immediate aftermath of the heroes' victory, Fury and the Secret Warriors quickly took their leave and went back underground. 

The Real Secret War 

For further information: Nick Fury, Agent of Nothing
 Time for the real conflict
Apparently, the Skrulls were just practice for the Secret Warriors, and Nick Fury revealed his true agenda to the team. It seemed he had been on the losing side of his conflict with HYDRA this entire time without realizing it. HYDRA was bigger and more far reaching than he ever realized. It even had its tentacles in S.H.I.E.L.D. while he ran it. However, the Skrull attack and the dismantling of S.H.I.E.L.D. hit HYDRA hard, giving Fury an opportunity to prepare for a new war against them while they reorganized. 

 With S.H.I.E.L.D. being replaced by H.A.M.M.E.R., HYDRA was moving to claim as many assets as it could before the U.S. government could, and the Secret Warriors knew that HYDRA would go after the Red Worm facility next. Red Worm was the psy-ops facility, and it was decided the Secret Warriors needed to get there first to prevent HYDRA from claiming such an asset. Unfortunately, HYDRA moved too quickly and the team arrived to witness Kraken and Gorgon personally overseeing the facility's evacuation. When they were in the process of executing two telepaths who were brain damaged by the rushed process of being awakened, Quake ordered her team to move in. This was a mistake. Kraken teleported away with the remaining telepaths, and Gorgon stayed behind to fight. He severely wounded Yo-Yo, chopping off her both her hands. Quake had to order a retreat.

This was a critical setback for the Secret Warriors and Fury's plans, as was the news that the Gorgon was even alive again. Yo-Yo's drastic injuries effectively benched her for the time being, leaving Quake to seek out a new recruit for the team. She traveled to the Australian outback along with Druid to meet with Eden Fesi, who was another name on Fury's list of Caterpillars. He readily agreed to join, with Gateway's permission, because he was not exactly thrilled with the lifestyle in the outback. Meanwhile, Fury reached out to Dum-Dum Dugan for help. Dugan and many former S.H.I.E.L.D. agents had private in the wake of H.A.M.M.E.R.'s takeover and formed a Howling Commandos private military company. Fury wanted them supporting the Secret Warriors.

Fury led the Howling Commandos on a raid of the Dock, another former S.H.I.E.L.D. base. This one housed the helicarriers, and Fury wanted them. While the Howling Commandos and H.A.M.M.E.R. fought, HYDRA intervened to prevent Fury from taking the helicarriers and all hell really broke loose. Then, the Secret Warriors arrived to back Fury up and turn the tide, making the raid on the Dock a success. HYDRA's forces retreated, the Howling Commandos made off with three helicarriers, and Fury recruited 3,000 H.A.M.M.E.R. agents over to his side. 
 
Despite saving the day, Fury kept the Secret Warriors in the dark about many things. Even the team leader, Quake, did not get the full story when she asked. It turned out that Fury was not the one who hit the panic button to call them into action at the Dock, but Fury would not provide any answers about that mystery. Similarly, it was implied by Gateway that Fury was running other Caterpillar teams, and for the time being, Fury was staying quiet about that as well. 

Dark Reign  

For further details: Dark Reign and God of Fear, God of War
Fury needed financing for his secret war and got it from using the Secret Warriors to rob a bank covertly being run by HYDRA. This act, coupled with HYDRA's defeat at the Dock, made Fury too much of a nuisance for Baron Strucker to ignore. However, Strucker still had much do, so he reached out to Norman Osborn to solve his Fury problem. 
 
 Dark Reign
Osborn lured Hellfire, Phobos and Eden Fesi into a trap using Black Widow as bait.  Phobos went in using a Nick Fury LMD as a disguise, getting caught in the trap and exposed. Hellfire and Eden came to the rescue, but it was Ares who gave the three the opportunity to get away. Phobos was Ares' son, and Ares was impressed with the way his son stood up to Osborn. This was only enough for them to get a brief moment before Osborn sent Ares, Hawkeye and agents of H.A.M.M.E.R. after them. Eden tried to teleport only them back to the secret base, but Ares forced the portal open to allow Osborn's forces to follow. It was chaos. The Secret Warriors, including Yo-Yo with her new bionic arms, found themselves fighting H.A.M.M.E.R., Iron Patriot, Ares and Hawkeye in their own base, which was going through an automated self-destruct countdown triggered by the intrusion. The Secret Warriors held off Osborn's forces and escaped through another one of Eden's portal before the base exploded. 
 
Meanwhile, Fury reached out to his old friend John Garrett. Together, they conned Osborn into helping them uncover an active agent of the long thought dormant agency of Leviathan.   

Wake the Beast  

For further details: Wake the Beast
 The Secret Warrior teams
The return of Leviathan complicated Fury's plans, but it also provided some opportunities. HYDRA and Leviathan quickly went to war, giving Fury extra room and time to maneuver his own forces. Quake discovered that her team was not the only team of Secret Warriors at Fury's disposal. Two others were active and operating outside of Fury's direct control. One was designated the black team and run by Alexander Pierce. This team was comprised of the more dangerous Caterpillars from Fury's list and tasked with watching HYDRA. The other was the gray team and run by Fury's own son, Mikel Fury. They were tasked with looking into Leviathan, which had been a seemingly dead end assignment until recently. Quake's Secret Warriors, the white team, were apparently meant as Fury's fist. 
 
Fury was preparing his forces to go operational when both HYDRA and Leviathan were at their weakest. He decided Druid was the weak link of the team and cut him from the roster against the wishes of Quake and the rest of the team. Meanwhile, no one realized that Hellfire had been compromised by HYDRA and was being blackmailed by Baron Strucker.  

Siege  

For further details: Siege  
 Joining the defense of Asgard
Fury's agenda was interrupted by Norman Osborn's sudden attack on Asgard and Steve Rogers' call for aid. He and the Secret Warriors answered the call. They allied with the assembled New Avengers and Young Avengers and came to the defense of the Asgardians. However, Phobos was left out of the battle and struck out on his own mission after seeing that his father had been killed by the Sentry
 
Osborn's forces fell, and when the full power of the Sentry's madness was unleashed, he was put down by the assembled heroes. What remained of Asgard was saved. The president turned against Osborn and H.A.M.M.E.R. for their actions, putting an end to the Dark Reign. But Fury and the Secret Warriors did not stick around for the aftermath. Once all was said and done, they returned to their secret war against HYDRA and Leviathan. 

Last Ride of the Howling Commandos

The time came for the major offensive against HYDRA Fury had been building toward. The target was Hell's Heaven, a secret HYDRA base deep inside the borders of China. Fury sent Team Black, led by Alexander Pierce, and two helicarriers full of Howling Commandos personnel, led by Dum-Dum Dugan, to carry out the assault. HYDRA's forces were overwhelmed by the attack. Team Black breached the facility's security along with a small unit of Howling Commandos and planted an explosive right in the heart of Hell's Heaven. Everyone exfiltrated back to the helicarrer's as the base was destroyed. 
 
Upon completing the objective, Pierce left with Team Black aboard a small aircraft, separating from the Howling Commandos to make their own way out of China and to their next destination. They were not present for what happened next. 
 
 The Commandos' last stand
Before making it out of China, the two helicarriers were intercepted by a superior HYDRA force led by the Gorgon. One helicarrier, the Argonaut, was shot down almost immediately. Dugan, commanding the other helicarrier, turned to fight rather than abandon the lost helicarrier by taking an opportunity to escape. However, they were still outgunned. Dugan's helicarrier also fell to HYDRA but not before HYDRA took some losses as well. The battle immediately resumed on the ground in the wreckage of fallen warships. An explosive injured Dugan, and Jasper Sitwell left the battle to get him to safety. Those who remained to fight HYDRA, including Gabriel Jones and Eric Koenig, were killed in action. 

Night

With the devastating battle in China, Fury's secret war had truly begun and the following six months only saw things worsen on all sides. The Howling Commandos were eliminated, and now, HYDRA came after the Secret Warriors. Fury's European command center was destroyed in an attack that also destroyed three city blocks of Paris. Their secret base in London was lost next due to a biological attack that claimed 12,000 civilian lives. The Secret Warriors were effectively crippled within two months. 
 
Night Falls
Once they were sidelined, the conflict between HYDRA and Leviathan escalated with both sides taking major losses. There was an attempted to call a cease-fire, but this resulted only in the assassination of Magadan, one of the three leaders of Leviathan. In retaliation, Leviathan destroyed HYDRA's new recruitment center in Seattle. This attack was so severe it devastated much of the American city and provoked Fury to find a way to get the Secret Warriors off the sidelines. 
 
Fury planned a simultaneous assault on both HYDRA and Leviathan. Team Black and Team Gray were to target two remaining major Leviathan bases while he and Team White went straight after Gehenna, HYDRA's principle base. The operation was meant to be quick and surgical. They would teleport in via Eden's power, plant the bomb and have Eden get them out all in under a minute. The mission did not go as planned. Baron Strucker, the Gorgon and Viper were expecting the Secret Warriors, and Eden was badly injured before he could teleport them out. The Secret Warriors fought rather than surrender, and Phobos used his prophetic knowledge to lead them to the escape path they were supposed to take. 
 
    Phobos vs Gorgon
A bridge collapse left Phobos and Fury separated from the rest of the team and on the side with HYDRA. Fury shot a line across so both of them could cross the chasm, but Phobos forced him to go alone. The son of war stood his ground and fought the Gorgon alone, because that was how it was supposed to be. He then died at the Gorgon's hands, because that was also how it was supposed to be. 
 
After bearing witness to Phobos' death, the Secret Warriors continued their escape. Time was limited. The mountain-breaker bomb they had deployed in Gehenna was armed and would soon explode. Finally, they found access to the surface, but HYDRA soldiers were closing in. Fury took the rear to provide cover and prevent them from being swarmed trying to board the aircraft waiting for them. The sheer numbers were against him, though. He was being overwhelmed until Hellfire came back for him. Together, they held HYDRA at bay until the bomb detonated. 
 
 Hellfire
As the mountain broke apart all around them, Hellfire lost his footing and began to fall into a chasm. Fury caught him just in time. Fury said that he knew Hellfire was the one who had tipped HYDRA off. He knew about the secret meetings with HYDRA agents. Hellfire explained that HYDRA had found him through the money they stole from that bank months back. They had backed him into a corner, and he was doing all he could to make sure that at least Quake survived. Fury said that he believed Hellfire and that the love between Hellfire and Quake was real. But then, he released Hellfire's arm and let the man fall. Catching up to the Secret Warriors, Fury said only that Hellfire did not make it. 
 
Druid rejoined the team, but after the losses of Phobos and Hellfire, Fury decided the team was no longer fit for duty and had Team White deactivated. 

Wheels Within Wheels 

Fury proceeded to make his final moves against HYDRA and Leviathan. He sent Team Gray to destroy the Hive's stronghold, and tragically, every member of Team Gray died in the operation, including Fury's son Mikel. Fury then allowed himself to be captured by HYDRA, knowing he already had them defeated. Kraken, as it turned out, was really his brother Jake Fury. They turned the tables on Baron Strucker, allowing Fury to personally execute him. His secret war was now over. 
 
The whole time Fury was waging his secret war, he was also manipulating world powers into deciding to give funding and jurisdiction to a new international peacekeeping force. It all came together after Strucker's execution. He folded the surviving members of Team White, Team Black and the Howling Commandos into this new organization and handed command of it over to Quake. He had completed his mission and decided it was time to walk away.

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