The series was originally solicited as a six issue limited series, but prior to the publication of the first issue, Marvel announced that this had changed and that Avengers: The Initiative would instead be an ongoing series, becoming the third regularly published 'Avengers' title from 2007 onwards, after the New Avengers and the Mighty Avengers.
The first group of young heroes have been sent to 'Hero Boot Camp' in Stamford, Connecticut, the site of the explosion that launched the whole Civil War. The issue largely follows the young heroes MVP, Cloud 9, Armory, and Trauma, as well as their drill sergeant, Gauntlet. MVP is established as one of the most capable young heroes there, and begins to express some feelings for the shy and self-conscious Cloud 9. During a training exercise, however, Trauma's powers accidentally cause Armory to lose control of her powers, and MVP is apparently killed pushing Cloud 9 out of the way. In response, they get rid of Armory's powers, and kick her out of the camp. Henry Peter Gyrich, who is overseeing the entire project, informs everyone present that the mishap 'never happened.'
While the recruits struggle to deal with the aftermath of MVP's death and Armory's wash out, Justice continues to be unhappy with Gauntlet's constant use of "New Warriors" as an insulting term. As the kids finish the obstacle course, Trauma again loses control of his transformation, first feeding off of Cloud 9's guilt at being responsible for the death, and then transforming into an image of a beaten and bloody Janet Van Dyne when Yellowjacket attempts to intervene. As Justice and Gauntlet clean up the situation, Dr. Pym is called to the lab where Baron Von Blitzschlag informs him and Gyrich of MVP's anatomy; instead of being enhanced by the Super Soldier Serum as everyone believed, he is actually an "Übermensch", the ultimate human specimen. As Blitzschlag and Gyrich laud the benefits of such a test subject, Pym again has a crisis of conscience, only enhanced when the German scientist recounts his past "villainous" acts and remarks "I am your greatest fan.
When a crisis over Texas, where the President is visiting, involving the HYDRA Terrorcarrier requires that the recruits join the fray, Cloud 9, Komodo, Hardball, Gauntlet, War Machine, Justice and Yellowjacket all arrive on the scene (with Hardball, Gauntlet and Komodo donning jet packs and Cloud 9 being revealed as the best marksman of the bunch when she receives a pulse rifle). As the attack escalates, Yellowjacket deploys the secret weapon he developed to infiltrate the carrier's shields, a small vibranium capsule inside of which he hides. When he breaches the shields, he grows to enormous size and forcibly redirects the carrier to crash, purposely riding it out. Meanwhile, Trauma, who had wanted the program to strip him of his powers and become normal again, is instead escorted by Gyrich to a room holding Beast and an unseen mutant who is a "specialist" who can help Trauma learn to control his powers. The "specialist" in question is the former mutant, Danielle Moonstar, who possessed similar powers to Trauma.
After the events of the Terrorcarrier incident, Hardball speaks to Komodo about Justice apparently having learned of MVP's fate. While he talks, he turns to see not Komodo but a strange girl sleeping next to him. Meanwhile Trauma and Danielle Moonstar discuss what training he will receive. Though the locals give Hardball a decidedly cold reception, a mysterious individual takes him aside and asks for information on S.P.I.N. Tech on which Komodo is currently being briefed. As the most promising of the new recruits, she is being given an official assignment to take down Spider-Man
S.P.I.N. Tech, as it turns out, is a new type of nanotechnology that, when fired in projectile form, can cause a superhuman to lose access to his or her superpowers instantly. When one of the Scarlet Spiders spots Spider-Man fighting Hydro-Man, The Shocker, and Boomerang, War Machine and Komodo head to the scene of the battle. Though Peter has everything well in hand, Komodo and War Machine arrive and cause the Sinister Syndicate to flee, and Spider-Man is left to battle the duo. He quickly incapacitates War Machine with a blast of webbing that shuts down his armor--but not before War Machine mysteriously states that even though Peter will be stripped of his powers, the world will not be left without a Spider-Man. While Komodo fares much better, Spider-Man's wit and a threat that her failure will result in her losing her powers causes a slip-up, which he uses to defeat her and slip away easily.
However, a mysterious third party, which War Machine calls "Red Team" and which has been cloaked during the fight, is revealed to be a group of people in duplicate versions of Tony Stark's Spider-Man armor. The story ends with Komodo's desperate plea not to be stripped of her powers, as she dislikes being normal and considers her other self to be a nobody.
Shortly after the Hulk returns from space with his Warbound, Hardball becomes involved in a covert operation to steal a piece of the S.P.I.N. technology. Meanwhile, Justice takes Cloud 9 to the Van Patrick home as part of her therapy, after the death of MVP. Upon reaching the home, both are shocked to discover MVP answering the door; though Justice and Cloud 9 are dispatched to where the Hulk's battleship appeared before inquiry can be given. With the missing cartridge of S.P.I.N. technology going undiscovered by Tony Stark; Stark's attempt to remove Hulk's powers during their conflict fail and Hardball is directly responsible for the early failure to contain the Hulk and prevent massive amounts of damage and casualties. Initiative members are assigned to protect the crowd and refrain from engaging the Hulk, though after Iron Man's failure; Rage instructs the team to disregard orders and engage Hulk and his Warbound, while Henry Peter Gyrich orders his secret team containing Bengal, Trauma, Constrictor, an unknown female Initiative recruit called Mutant Zero and the Scarlet Spiders to the conflict to save the Initiative trainees.
The Shadow Initiative sneaks into Madison Square Garden, where the Hulk has built an arena to deliver captured heroes for their punishment. It is there where they are confronted by some of the Hulk's Death's Head guards, and Mutant Zero defeats them all. Across Manhattan, Hank Pym, along with Justice and O*N*E Sentinels, who left the X-Men, were setting up the devices that is a part of Iron Man's plan to fully send all of Manhattan and those who live in it into the Negative Zone. Trauma then transforms himself into Thor; this was due to Korg's fear of the Thunder God. While Cloud 9 nearly kills Elloe by filling her lungs with smoke, however, she is stopped by Trauma who sees this.
Soon the team is confronted by the Hulk, who then defeats almost all of the Shadow team members. Trauma tries to defeat the Hulk in various forms of the Hulk's enemies, but when the Hulk won't flinch at the sight of his old foes; this leaves Trauma as a weak human. Later on in the hospital where Trauma is recovering, he makes amends to his former teammates, especially Hardball and Cloud 9, while Danielle Moonstar shows Gyrich of Trauma's failure. In that move Gyrich then demotes Trauma from an Omega threat, which Gyrich first saw him as, to a Class 50.
Taskmaster is seen studying MVP's and Spider-Man's moves, in order to teach the MVP clones, in their role as Scarlet Spiders.
Since the results of the previous clonings of MVP impressed Initiative administrators enough to attempt to fill places within the Fifty State Initiative with further clones of MVP.
Justice, Debrii, Slapstick, Rage, MVP and the two remaining Scarlet Spiders left the Initiative to form Counter Force, described as a counter-initiative that will dedicate themselves to keeping the government program honest.
Later 'Yellowjacket-Skrull' gives orders to Gauntlet to dispatch the cadets to help the Young Avengers fight the Skrulls, and Proton is killed during the battle. The Skrulls defeat the cadets and Young Avengers, but then Nick Fury arrives with his "commandos. Meanwhile Ant-Man (Eric O'Grady), the only cadet still on Camp Hammond witnessed how "Yellowjacket" welcomed a Skrull commander to the base and during the big fight against the Skrull army, Crusader, (a Skrull who lives on Earth and an Initiative cadet) decided to fight for Earth.
After defeating a Skrull imposter looking like 'She-Thing', 3-D Man joined up with the Skrull Kill Krew and found out that in every Initiative state team is one Skrull-imposter and decided to kill them all. Komodo joined the team as well.
The Initiative program denies all knowledge of a special Black Ops Team. There is no pardon on file for the super-villain known as the Constrictor. No record of any dealings with the Vietnamese national codenamed Bengal. Tony Stark cannot recall what became of his designs for the Iron Spider armor. And, most importantly, the Superhuman Armed Forces wishes to dispel all rumors of a 199th mutant. We repeat, there is no Mutant Zero. Mutant Zero does NOT exist. That is all.
This Shadow Initiative was sent out by Henry Gyrich to free the Initiative members captured by the Hulk's Warbound; Rage, Cloud 9, Ultra Girl, Thor Girl, Slapstick and Hardball. On this assignment Bengal showed to be a perfect field leader of this Shadow Initiative.
The black ops group successfully rescues these captured trainees, while Trauma, their "secret weapon" tries to use his powers to scare the Hulk (becoming, in turn, the Abomination, Juggernaut, Brian Banner, and Bruce Banner). He fails to beat the Hulk, and the Hulk beats him into unconsciousness, leaving Terrance alive to pass the message on to the others. Trauma is later seen recuperating in the Initiative's medical bay.
It is later revealed that the Scarlet Spiders are clones of Michael Van Patrick (MVP), a deceased initiative recruit accidentally killed. The Scarlet Spiders are later taken off the Black Ops team after revealing themselves to the public and placed with the other trainees.
Gyrich called them to protect him from K.I.A., but they lost and one of the Scarlet Spiders was killed, and Constrictor was badly maimed. Mutant Zero saved Gyrich and Scarlet Spiders continued the battle for their brother.
After KIA was defeated, the two remaining Scarlet Spiders left the Initiative to join Counter Force, a team of former New Warriors, MVP and these two, led by Justice, while Constrictor was healed with two bionic hands.