BIOGRAPHY page 5
In those few days, the world was turned upside down. A series of catastrophes and trouble spots led Congress to invoke the S.H.I.E.L.D. Act, turning national authority over to the Director of S.H.I.E.L.D. for the duration of the emergency. Once they did, Steve Rogers revealed he was actually the Hydra Supreme and had helped manufacture these crises. Now the legally recognized authority in the United States under the Act, Rogers refused to give up his emergency powers and ushered in the Hydra era of America. Inhumans were declared a potential threat to national security, and were to be rounded up on sight. Coulson never made the meet, and so Quake had to prepare her own plan for dealing with the situation.
Queen Medusa had taken most of the Inhuman Royal Family out into space to search for the origins of Terrigen after the cloud was destroyed. Daisy decided to locate and rescue Karnak, one of the last Royals on Earth and a master strategist. She reached out to the NuHuman network and received help from Ms. Marvel, Moon Girl and Devil Dinosaur in attacking a prison convoy looking for Karnak. They didn't find him, but they did release Dante Pertuz (Inferno), a NuHuman with ties 
to the Royal Family. After the deaths of Moth Squadron, Daisy wasn't interested in opening herself up to a new team, but she needed allies. This loose association of NuHumans located Karnak at the Inhuman detention camp Inferno to which she was being transported. Quake was completely mission-oriented, and intended to sneak in and rescue Karnak alone, but Ms. Marvel insisted they free all the Inhuman captives at the base. [Secret Warriors (2nd series) #1]
Karnak declared they needed a specific Inhuman named Leer to save the Inhuman race. Leer was being held in New Tian territory, the sovereign mutant state on the west coast in opposition to Hydra's government. Following a tense encounter with the X-Men running New Tian, Quake's 
group located a secret laboratory being run by the Dark Beast, performing human experimentation. Despite Dante and Ms. Marvel's objections, Quake and Karnak locked themselves in a vault with Dark Beast and tortured him until he revealed Leer's location. McCoy had been coordinating with Hydra and gave the boy back over to their care. [Secret Warriors (2nd series) #2-3]
In their search for Leer, Quake was forced to confront her father, as Mister Hyde was working for Hydra as a commandant. Hydra had turned New Attilan into a prison colony, holding many of the prominent remaining Inhumans there. Daisy also learned that Karnak had misled her -- Leer was 
actually Karnak's son, whom he had turned over to Mister Sinister and Dark Beast in an effort to artificially recreate Terrigenesis now that the Terrigen cloud was gone. Karnak believed Leer was key to saving the Inhuman people, not from Hydra, but from stagnation and extinction. Unable to strike at Rogers directly now, Daisy rallied the Inhuman prisoners around her team of "secret Warriors" and led them in an uprising against Hydra. The Inhumans were freed and Mister Hyde was taken down by Daisy and her team. [Secret Warriors (2nd series) #4-5]
As the dust settled and S.H.I.E.L.D. was declared defunct after Hydra's infiltration, Daisy learned that Phil Coulson was killed by Deadpool at the start of the takeover. She got Taskmaster and Bullseye to help her set up Wilson, and planned on killing Deadpool to take revenge for Coulson. 
Deadpool fought back but, when Quake was set to entomb him forever in cement, he accepted responsibility for Coulson's death. In his own way, Deadpool tried to console Daisy that she was doing the right thing and she shouldn't regret murdering him later. Before she could finish the job, though, Moon Girl stepped in and convinced Daisy not to go through with it. Her team needed her to do what Coulson taught her to do: save lives, not take them. [Secret Warriors (2nd series) #6-7]
Inferno's infant niece Ariela had been kidnapped by McCoy so he and Sinister could lure out Karnak for not fulfilling his end of their bargain. Quake and the Secret Warriors discovered Dark Beast had kidnapped dozens of potential NuHumans for his experimentations. They were joined by Magik of the X-Men, who regretted McCoy escaping on her watch. The villains escaped with Dante's niece, but the Warriors recovered the NuHuman children and started returning them to their parents. When they did, however, the children were revealed as suicide bombers, genetically and behaviorally programmed by Sinister to smear the Inhumans. The Secret Warriors became wanted fugitives for their apparent role in the kidnappings and deaths. [Secret Warriors (2nd series) #8-9]
Iso, current ruler of New Attilan, allowed the Secret Warriors to hide out there while they tried to figure out how to clear their names. Inferno was still fretful over his missing niece, and Karnak was avoiding them. Daisy went to comfort Dante alone and they ended up jumping into bed together, 
which only got more awkward once Ms. Marvel stopped by to check on Dante. Daisy told Dante that MM had a crush on him and that he handled it badly when she came to the door. She also coldly dismissed their time in bed as a one-time thing to relieve stress, leading Dante to storm out on her. Inferno ended up stealing a piece of Terrigen crystal from New Attilan, hoping to trade it to Sinister for his niece. [Secret Warriors (2nd series) #10]
Iso and New Attilan blamed the Secret Warriors for Dante's actions, forcing Daisy and the others to flee through one of Magik's portals. They caught Dante making the exchange with Sinister, but only managed to retrieve Ariela as Dante went off with Sinister to fulfill their deal and serve in his experiments. Karnak finally responded to their requests for aid but, while he was indifferent to Inferno's fate, he refused to allow Sinister to have access to Terrigen. Karnak only intended to allow Sinister and Dark Beast to get close to recreating Terrigen, then take their work and go the rest of the way himself. With Karnak explaining the threat involved, Daisy was able to convince Iso and the rest of the Inhumans to join them in an attack on Sinister to rescue Dante and recover the Terrigen. Sinister was defeated and his work recovered, but the Inhumans all rejected Karnak's amoral and draconian efforts to secure their future. Daisy and the Secret Warriors were accepted by New Attilan again, but Karnak and Dante (for his theft of the Terrigen) were expelled entirely. [Secret Warriors (2nd series) #11]
In the aftermath of the Sinister affair, Moon Girl tried to keep her team together by individually inviting them all over to her house to "babysit" her. At Moon Girl's insistence, they all tried to mend fences over a game of Risk. Dante learned Ms. Marvel didn't have a crush on him -- she just had a really low opinion of Daisy and thought he could do better. Daisy apologized to Ms. Marvel for torturing Dark Beast. She wasn't proud of her actions and hoped, in the future, she could be more 
of a hero like MM. Daisy apologized to Dante as well, and it seemed like there might be some real feelings on both sides. She was so torn up over the deaths of Yo-Yo, Coulson, Fury and others in her lie that she was afraid to admit that before now. Daisy kissed Dante again before the night was over, but said she needed to work on herself some more before she got together with anyone. Still, she told him to look her up in six months or so. The Secret Warriors did not remain together, but the bonds they forged during their time as a group remained. [Secret Warriors (2nd series) #12]
Daisy remained in contact with Nick Fury, Jr., despite the downfall of S.H.I.E.L.D. She was seen with a group of heroes hunting down the Punisher, who had sided with Hydra during the takeover and absconded with the War Machine armor. [Punisher (2nd series) #224-227] She worked with Nick Fury again opposing the Punisher when he brought his war back to New York. [Punisher (12th series) #16] With S.H.I.E.L.D. still dismantled and having little life outside of the espionage world, it remains to be seen where Daisy Johnson will pop up next.