Despite their exchange, Iron Man came to Ms. Marvel to be the field leader of the new, official Avengers roster under the Superhuman Registration Act and the Fifty States Initiative. As Director of S.H.I.E.L.D., Tony recognized he didn't have the free time to lead the Avengers as well, and he wanted Carol to do it. Carol's recent troubles made her reluctant to accept the responsibility. She was actually prepared to reject the offer and told her publicist Susan Day she was going to let her go as well. Susan called Carol out on her own lack of direction, pointing out she could only publicize what Carol was doing, and Carol hadn't pursued much since retaining her services. Carol needed a goal, a mission, something to focus her attention.

Taking the initiative, Ms. Marvel accepted Iron Man's offer and worked with Tony to assemble the best roster of Avengers possible from the Initiative registration files. However, she also negotiated for her own autonomous strike team, taking authority from Tony to use S.H.I.E.L.D. resources and personnel as she saw fit. This independent unit, dubbed Operation: Lightning Storm, would be more proactive than the Avengers and less bogged down by bureaucracy than S.H.I.E.L.D. With her new mandate, Carol and Lightning Storm took down the A.I.M. cell responsible for the DNA bomb, giving Susan plenty of material to publicize Ms. Marvel and her new venture. Ms. Marvel established a mobile base of operations for Lightning Storm from Minicarrier 13 and, considering the damage continually done to her apartment by the likes of Traveler, Rogue and Warbird, moved into the Minicarrier's crew quarters on a permanent basis. In addition to Wonder Man's assistance, she crewed Lightning Storm with S.H.I.E.L.D. agents Sum (from special operations), Baines (from tech), and Locke (from psy-ops). [Mighty Avengers (1st series) #1, Ms. Marvel (2nd series) #13]

Before she could move forward, though, Carol had to correct some wrongs from her recent past. She and Wonder Man coordinated with Tony, securing a future for Julia Carpenter, still a fugitive after the final battle of the Superhuman Civil War. Arachne was offered a position with Omega Flight, a joint Canadian-American initiative outside U.S. territorial boundaries so she didn't have to register, and she was reunited with her daughter. This did NOT mend fences between Carol and Julia, but she thought it was important anyway. Carol also spoke with Ana, who told Carol she didn't blame her for the injuries she suffered facing Doomsday Man. Araña wanted to continue working with Ms. Marvel, but Carol would not violate the restraining order and Mr. Corazon's wishes. [Ms. Marvel (2nd series) #13-14]

Ms. Marvel found The Mighty Avengers (branding by Susan Day) difficult to wrangle, but the new team was put through its paces against several major threats such as Ultron, Doctor Doom and invasions by the Hulk and a swarm of symbiotes. Iron Man continued to exert his authority over Carol's team while refusing to officially lead, however. Jessica Drew had been a fugitive member of the unregistered Avengers as Spider-Woman, but Tony not only pardoned her crimes when she came in from the cold, he insisted on her being placed on the active Avengers roster. [Mighty Avengers (1st series) #1-11, World War Hulk #1-5]

Despite her progressing personal relationship with William Wagner and the success of Operation: Lightning Storm, Carol got little respect from SHIELD deputy director Maria Hill. She basically accused Carol of sleeping with Tony Stark and being his "favorite blonde" in order to get Lightning Storm's authorization. She pushed Ms. Marvel into following up on the A.I.M. cell from Indianapolis in order to prove she was worthy of commanding a S.H.I.E.L.D. detachment. Lightning Storm uncovered evidence of a civil war among A.I.M. factions led by M.O.D.O.K. and Monica Rappaccini, with M.O.D.O.K.'s illegitimate son Sean Madigan stirring things up in the middle.

Madigan used the DNA bomb to lure all factions to his purported employers, A.I.M. agents interested in overthrowing M.O.D.O.K. During the free-for-all that followed, M.O.D.O.K. turned his telepathy on Wonder Man and mind-controlled Simon into trying to kill Carol. Unable to talk him down or outfight him, Ms. Marvel took the unusual tactic of grabbing Wonder Man into a full embrace and passionate kiss. As Carol and Simon awkwardly separated, they returned to the scene to find Madigan and M.O.D.O.K. had escaped with the DNA bomb while Agent Locke burnt out her psy-bernetics incapacitating the remaining A.I.M. agents.

The captive Monica Rappaccini updated Lightning Storm on Madigan's machinations, but they were still caught off-guard when he rigged the G-TAC Scrambler to M.O.D.O.K. himself and deposited the Scientist Supreme in the middle of Times Square. As the DNA bomb detonated, Ms. Marvel tried to fly M.O.D.O.K. out of range of civilians. Her genetic code was horribly disfigured by the waves coming off the bomb but, as with the Targoth infection, Carol proved surprisingly resilient. This time, however, she heard voices in her head talking about her healing factor, while her body temporarily turned blue.

Although M.O.D.O.K. and the DNA bomb were disposed of successfully, Operation: Lightning Storm seemed on the verge of breaking. Monica Rappaccini killed Agent Baines before escaping, and Agent Locke was crippled and placed on permanent medical leave due to her psy-bernetics incident. Carol also implicitly told Simon to give her space for a time, as it was clear he wanted to pursue newfound feelings from their kiss, but she was uncomfortable with that. On top of it all, the Daily Bugle ran a front page spread of the kiss, and so Carol assumed that was why William Wagner stopped returning her calls. Victory felt a lot like defeat this time. [Ms. Marvel (2nd series) #15-17]

Ms. Marvel continued her duties with the Initiative and the Avengers. She sponsored an Initiative trainee named Ultra Girl, another heroine with Kree-based powers. When she graduated from Camp Hammond, Carol gave Suzy her original Ms. Marvel uniform to wear. [Avengers: The Initiative #12] Carol was also involved in a time travel adventure with the registered and unregistered Avengers joining forces with the displaced Invaders of World War II. [Avengers / Invaders #1-12] Finally, she had to deal with Iron Man's alarming news that humanity may have been infiltrated by shape-changing Skrulls as part of a larger invasion. This significantly colored her reunion with Captain Mar-Vell, who had seemingly emerged from the Negative Zone from some point in the past before his death by cancer. The Skrull threat made Ms. Marvel and Iron Man suspicious and they tried to contain Captain Marvel. However, Mar-Vell escaped their custody, leaving their questions unanswered. [Captain Marvel (6th series) #1-5]

Carol had several passing encounters that would prove important to her in the months to come. Her constant watch on A.I.M. activities alerted her that one cell had located Gavin, the boy from the Storyteller program. She reached Gavin first and found his reality-warping abilities had grown in strength, allowing him to make virtually anything happen with a spoken narrative. She gave Gavin a warning about A.I.M., but he disappeared again, leaving his fate inconclusive. [Ms. Marvel Special: Storyteller #1] Carol also ran across the unregistered hero Spider-Man and attempted to bring him into custody. Their registration issues were put aside for a team-up, however, as junk robots began spontaneously assembling themselves on the streets of New York. They discovered the billionaire technologist Stuart Cavenger had uploaded his consciousness to the internet, with different aspects of his personality wirelessly inhabiting separate and squabbling robot bodies. The Stuart of Destruction was decapitated and taken into custody. Spider-Man and Ms. Marvel found they worked well together, despite how irritating he was to Carol. [Ms. Marvel Annual #1]

Seeing how vulnerable even trained S.H.I.E.L.D. agents were in Lightning Storm's missions, Ms. Marvel requisitioned full-fledged Initiative super-heroes to restock her ranks. Well, Maria Hill technically fulfilled that request by sending her Machine Man, a sarcastic robot with a knack for annoying "fleshy ones," and Rick Sheridan, whose alter ego Sleepwalker could only appear when he was asleep. Carol also repaired her friendship with Hank McCoy while looking into the mysterious healing factor that kept saving her life.

Ms. Marvel stumbled into an operation that was apparently trying to kidnap superhuman females. Lightning Storm uncovered the Puppet Master operating a human trafficking auction house out of Chile. Masters tried to take control of Ms. Marvel as well, but her new healing factor rejected his power. Carol was shocked to discover Araña had been taken by Puppet Master without her knowing it. As Ana fought Ms. Marvel and tried to shake her mind control, she unwittingly referred to Carol as her mother, surprising Carol at how deeply Ana felt their connection. Ms. Marvel pursued Puppet Master into his stolen castle, freeing his puppets as she went. She confronted Masters and learned he had rigged his headquarters with explosives, knowing he would inevitably be found out, but hoping to eliminate any heroes who tried to capture him in one suicidal blast. Utterly disgusted and trusting in her healing factor, Carol made a conscious decision not to stop Puppet Master from triggering his bomb. She let him kill himself knowing she would survive the blast, but lied to her teammates about it afterwards. [Ms. Marvel (2nd series) #18-20]

The secret of Carol's healing factor made itself known when Cru stormed Minicarrier 13 and made off with her. In the explosion over Spaulding months ago, a fragment of Cru's techno-organic rebuild and repair protocols became lodged into Carol's system. It worked for the benefit of Carol's physiology while Cru spent months reassembling herself from scattered pieces in the upper atmosphere. Cru brought Carol to Monster Island, where a second Brood ship had landed that same night. It carried to Brood Queen Carol thought she had killed years ago as Binary, now a form of living indestructible crystal hoping to create a new hive on Earth.

Cru needed to reabsorb her repair and rebuild protocols from Carol before confronting the Brood Queen, but they were uncovered during the process and forced to separate, leaving them both temporarily powerless. Agent Sum, Wonder Man and Araña arrived with Lightning Storm to back them up, giving Cru and Ms. Marvel time to reconnect. Cru was forced to expedite the assimilation process, maxing out Carol's powers and restoring her Binary levels, although she warned it might turn out to be a curse rather than a gift. The Brood Queen murdered Cru before she could explain further, and Carol engaged the first foe she ever fought as Binary. Taking advantage of the Queen's indestructibility, Carol drew her up into space and lit up a nuclear power drive in her mouth, launching the Brood Queen out into the cold vacuum of space to drift forever. [Ms. Marvel (2nd series) #21-24]

A situation arose when Tony Stark recorded Carol Danvers' presence in Avengers Tower at the same time Ms. Marvel and Lightning Storm were on Monster Island. Stark recognized this meant a Skrull was actively impersonating Ms. Marvel. Worse, he was unable to contain Carol on the Minicarrier once she returned to New York, leaving them unable to verify which Carol was which after that. Meanwhile, Carol was trying to catch up with her personal life. She tried calling William Wagner, only to learn he was supposedly with her at that very moment. Ms. Marvel raced to William's address, but he was dead by the time she arrived, and Agent Sum burst in to take her into custody as a potential Skrull. [Ms. Marvel (2nd series) #25]

Carol and her Skrull doppelganger were eventually captured fighting together by Operation: Lightning Storm. On-board the Minicarrier, Ms. Marvel realized Agent Sum had also been replaced by a Skrull. She convinced her team of her true identity and they pushed "Sum" into revealing himself, leading to the death of the Super-Skrull. The "Carol" Skrull then sent Ms. Marvel on a wild goose chase thinking William might still be alive just to torment her, before blowing herself up using copied Super-Skrull powers from Nitro. The Minicarrier was totally destroyed and most of Lightning Storm's support staff died in the blast.

Ms. Marvel was in an awful place mentally after William's murder and the deaths of her team, and she flew to Wonder Man for comfort. She confessed to Simon that she felt like a horrible person, about how she let Puppet Master die, how she tried to kill Warbird and Doomsday Man but couldn't finish the job, and so on. Simon refused to let Carol beat herself up, and she threw herself at him in order to feel something good. Their night together was a mistake, and washed away with the morning light as Ms. Marvel received a priority alert from Iron Man for the Avengers to assemble. [Ms. Marvel (2nd series) #26-27]

[Note: Mighty Avengers (1st series) #6 presented Carol and Simon as if they were in a full relationship. According to the timeline in Ms. Marvel, however, this never actually took place.]

The Avengers were called to the Savage Land to investigate the landing of a possible Skrull ship. Both the registered and unregistered teams arrived to find an anachronistic batch of Earth heroes emerge from the vessel, signifying they were either Skrulls or had been replaced by Skrulls years ago. At the same time, a full invasion of Earth began with all the StarkTech in S.H.I.E.L.D. and Avengers Tower crippled by an alien virus, and Super-Skrulls attacking Manhattan. Nearly crippled himself by the virus, Iron Man dispatched Carol back to New York while the others dealt with the Savage Land. Paranoia was high among the heroes of New York, though -- when Nick Fury arrived with a team of Secret Warriors as reinforcements, he evacuated his team with the Young Avengers and Initiative recruits present. Fury thought Ms. Marvel was a Skrull, however, and blasted her away before teleporting out with his team, leaving her to face the Skrulls alone. Carol fought for hours against the Skrulls and Super-Skrulls in New York. [Ms. Marvel (2nd series) #28-30, Secret Invasion #1-5]