Prologue:
Lincoln wasn't on board the Quinjet with Hive, but, thanks to Daisy's vision of the future, he was still able to fry the manual controls of the jet before getting off it back on Zephyr One, ensuring that Hive would still die, only with no one from SHIELD dying with him. Due to this, Lincoln and Daisy were able to rekindle their romance and Lincoln helped Daisy get back her sanity, allowing her to return to the field. SHIELD was reauthorized as a legitimate agency shortly after, under a new director and public face, Jeffrey Mace, while Coulson continued to run things from the background as field commander, with May continuing to act as Coulson's right hand.
Jemma was promoted to Special Advisor to the Director In Science and Technology, giving her higher clearance, since Mace had reinstated the clearance levels, only by color rather than number, something about not wanting agents to feel degraded or undervalued. This had caused a few rifts to be formed between her and the rest of the team, especially Fitz, since they were all reluctant to share things with her, due to how close she was to Mace and they didn't necessarily trust him at first, so it was hard to trust her with anything secret. However, Jemma had eventually managed to regain the team's trust after putting an end her lie detector tests.
Daisy, Lincoln and Mack had assumed to control over the Zephyr One, traveling all over the world, responding to sightings of inhumans and other powered individuals, containing them and registering them under the Sokovia Accords, which Daisy and Lincoln had both agreed to sign. Daisy was also put in charge of the Inhuman Registry, since as SHIELD's top inhuman agent, she was seen as the best one who could do the job and she used the registry to select members for the rebooted Secret Warriors initiative, since now that Hive was gone, the team was cleared for duty, which was good, since with the Avengers being a defunct team at the moment with Captain Rogers and his associates on the run, the world was even more vulnerable and the Secret Warriors had almost become the new Avengers, since they all had powers and were dedicated to using them to help others.
Mace had soon proved himself an adequate director, since while he still relied on others, like Coulson for tactical support, Jemma for scientific expertise and Daisy for inhuman relations, Mace was quite adequate at dealing with the political side of SHIELD. He had gotten the zoning approved for SHIELD to build a larger, more advanced headquarters in DC, building a new base out of the remains of the Triskelion. He was also able to use his diplomatic skills to come to a compromise and rewriting of the Sokovia Accords so that it was a better compromise between both sides of the Avengers Civil War, leading to all charges being dropped and the reunification of the team.
As time went on, things for the team began to change. Daisy and Lincoln had gotten married a couple of years after SHIELD's reauthorization and lived in DC, where they were both stationed at the Triskelion, Daisy as a field agent and Lincoln as a medic. They lived in a suburban house, raising a family together, with their daughter, Skylar and their son Drake and they even had a dog, a golden retriever named Lucky, who Daisy had gotten for Skylar for her 6th birthday, adopting the dog from her father's pet clinic. Skylar, or as her parents and most of her friends called her, Skye, was 15 and she had undergone terrigenesis willingly at the age of 12 and gained powers of energy manipulation, similar to that of Lash, only without the part of turning into a monster and she could do more than just blast holes into things and people. Drake had was 12 and had just undergone the terrigenesis process, resulting in him gaining the ability to manipulate and control technology.
Fitz and Simmons had also gotten married and were also living in Washington DC with their son William Fitz. While Fitz had wanted to get a monkey for their home, Jemma had firmly put her foot down on that idea, saying that she wasn't going to tolerate any monkey business from her husband or son and she as sure as well wasn't going to up with any from an actual monkey. So they had compromise with a pet cat that Fitz was allowed to name Monkey, since Jemma was not a dog person.
Mack and Elena had gotten married, though they were actually living in Miami, since Elena wanted to be closer to her roots. Mack worked as the commanding officer of the SHIELD base Nexus, which had become SHIELD's new storage facility for alien artifacts and Elena ran inhuman registration in Florida, since Mace had decided that once they had recruited enough inhumans into SHIELD, that one would be placed in each state to head registration in said state. Mack and Elena also had a daughter, Hope, who, like her mother possessed the inhuman gene, however, both of her parents wanted to wait until Hope turned 16 at the very least before undergoing the terrigenesis process.
Coulson and May had eventually realized that they had feelings for each other and after dating for a few years, they eloped in Vegas, with Daisy being their main witness, since she was already like a daughter to both of them and she thought of them as her parents, so much so that Daisy had actually asked Coulson to walk her down the aisle at her own wedding, which he did. They continued on with May's original plans from before Bahrain to expand their family, which they did into 3 kids, Nicholas, Andrew and Skye. And of course, Daisy was practically like their oldest kid.
Eventually, The SHIELD Academies were reopened, but in new secure locations and for the younger children of agents and for young inhumans, Daisy left the line of field work to establish the SHIELD Youth Academy in the outskirts of DC, under a cloaking dome, in order to keep it secure from the outside world, while not creating a feeling of isolation for the people within it's walls.
