Following the revelation of HYDRA's continued existence during the Battle at the Triskelion and the subsequent war, S.H.I.E.L.D. was left in shambles and publicly declared a terrorist organization. Only two groups of S.H.I.E.L.D. agents remained active, one led by Phil Coulson and stationed in the Playground base, and the other led by Robert Gonzales, stationed on the aircraft carrier Iliad. The two groups did not know about each other, and they had completely different ideas about the future of S.H.I.E.L.D.
The Two S.H.I.E.L.D.s
After the HYDRA Uprising, both Phil Coulson and Robert Gonzales started working on rebuilding S.H.I.E.L.D. But while Coulson had the official blessing for his task from the former director Nick Fury, Robert Gonzales believed that Fury was dead since the day the Winter Soldier attacked him. The core of Coulson's organization was his old team, who managed to defeat the forces of HYDRA led by John Garrett at the Battle at Cybertek. On the other hand, Gonzales' men were the remaining loyal crewmembers of the aircraft carrier Iliad and a few professors and students from the S.H.I.E.L.D. Academy.
Right from the beginning, Coulson and Gonzales led their factions completely differently. While Coulson mainly continued with Nick Fury's way of leading S.H.I.E.L.D., Gonzales instead made a board of leaders, sharing duties and responsibilities with his fellow high ranking agents. Every important decision had to be put to a vote, because they all agreed the leadership should operate with transparency and not from the shadows.
Once Robert Gonzales and his men found about Phil Coulson's organization, they dispatched Agents Isabelle Hartley, Bobbi Morse and Alphonso Mackenzie to join Coulson's S.H.I.E.L.D. to gather intel. What they reported convinced Gonzales and his board that Coulson's ideas of running S.H.I.E.L.D. were too similar to Fury's.
While in Coulson's S.H.I.E.L.D., Hartley was killed in action by a gifted man named Carl Creel. Mackenzie worked as a simple mechanic in the garage of the Bus while secretly searching for Fury's Toolbox. Agent Morse worked in the field completing many assignments. They included infiltrating HYDRA, assisting in the manhunt for Grant Ward, interrogating Sunil Bakshi, and stopping HYDRA from starting a disaster.
Eventually, Lance Hunter, Coulson, and Melinda May became suspicious about Mackenzie and Morse. When Mackenzie could not explain to Hunter what he was doing, he knocked Hunter unconscious and had him secretly brought aboard the Iliad. There Mackenzie them explained that he was working for "the real S.H.I.E.L.D.". As Hunter was a good friend of Mackenzie, the ex-husband of Morse, and had previously gone to great lengths in a failed attempt to save Hartley's life, Gonzales greeted him kindly and explained the origins and mentality of his S.H.I.E.L.D. Gonzales reminded Hunter of how Coulson had seemingly gone insane due to the alien DNA now in his blood and how he was responsible for Isabelle Hartley's death due to his relentless search for the Obelisk, something which killed Agent Antoine Triplett and caused mutations for Raina and Agent Skye. While Hunter remained loyal to Coulson, he was able to agree with Gonzales about many of the risks involved with following Coulson.
After Lance Hunter had escaped the Iliad, Bobbi Morse suggested that they should attack the Playground as soon as possible. Morse returned to the base and prepared for the attack. While Phil Coulson interrogated Alphonso Mackenzie about his loyalties, Melinda May surprised Morse in the act of stealing the Toolbox. She tried to stop Morse but failed due a blackout Morse caused. Coulson had then learned that Mackenzie worked for another organization, and he and his agents tried to capture Mackenzie, but he escaped in the blackout.
Then, Jemma Simmons succeeded in capturing Morse but her victory was short-lived. While a dendrotoxin in a gas state was circulated through the ventilation ducts, the wall exploded from the outside by Robert Gonzales' S.H.I.E.L.D., and they stormed the base.
Later, they captured all members of Coulson's S.H.I.E.L.D. faction. All the agents in the area eventually surrendered to Gonzales's agents. They succeeded in capturing Coulson, who was brought to Gonzales for a discussion about the Toolbox. When Gonzales gave the Toolbox to an subordinate, Melinda May surprised Gonzales and his agents by neutralizing them and giving Coulson a way to escape the base, and also warning him that Gonzales planed to put their hands on Skye.
After the success of the capture of the Playground, Robert Gonzales discovered that Phil Coulson had taken Skye to the Retreat. Since he feared her and her powers, Gonzales ordered Bobbi Morse and Tomas Calderon to retrieve her.
Melinda May heard their plan and contacted Skye and told her the situation. Skye left the Retreat and ran into the woods.
Morse and Calderon landed near the Retreat. Morse reminded the agents that Skye was a S.H.I.E.L.D. agent just like the rest of them and to use the non-lethal I.C.E.R.s only; however, Calderon ignored her order and took a real gun.
In the woods Skye encountered one of the agents and a struggle ensued with a gun being fired off. Morse and Calderon headed in the direction of the shot and called for backup. Skye managed to defeat the agent and took his sidearm. Calderon, seeing this, fired his real gun while Morse desperately tried to warn Skye, but to no avail. However, Skye deflected the bullet with her powers and caused a shockwave knocking Morse and Calderon back and destroying the surrounding area. Calderon was also impaled in the shoulder by a piece of flying wood. Skye, horrified by her actions, called Gordon's name; he came and took her away from the chaos.
Once Coulson and Hunter arrived to the Retreat, they planed what to do next. Coulson triggered the alarm, notifying Gonzales of his location. Gonzales' agents arrived, got out an Electronic Battering Ram and started to hit the door so they could knock it down. Coulson used Holographic Cards to project a hologram of him and Hunter playing cards to trick the agents.
They were able to take down all of the agents with I.C.E.R.'s and proceed to outside the Retreat. Outside, they were confronted by more S.H.I.E.L.D. agents that were in shielded Quinjets. They were taken into the Quinjet and were about to be taken back to Gonzales.
Right before the Quinjet doors closed, Deathlok, Coulson's reinforcement, arrived and took down all the agents that had captured Coulson and Hunter. Deathlok then used his arm cannon to take down the other Quinjet. They escaped the scene.
Hunt for the Fugitives
Melinda May was hold in Vault D. In the meantime, Robert Gonzales asked Leo Fitz and Jemma Simmons to open for him the Toolbox. They refused and Fitz left to pack his bag to leave. Morse seemingly convinced Simmons to stay and help to open the Toolbox. Instead, Simmons replicated the box in order to smuggle it out of the Playground with Fitz. When Fitz learned what she was doing, he covered her actions and convinced Alphonso Mackenzie and Morse that Simmons was in earnest. Fitz eventually left with the Toolbox. But Gonzales' S.H.I.E.L.D. appointed agents to tail him.
May asked permission to run the Playground. There, May was amazed to discover how many secrets Phil Coulson had kept from her, including Theta Protocol. Alphonso Mackenzie theorized that its a program of training powered people led by Coulson. May heard enough and ordered Simmons to open the Toolbox.
Jemma Simmons discovered May about the switch she had made. So in order to find Coulson, May ordered Simmons to hack Deathlok's hardware. In the meantime, Skye called the base and told May that she was with her father and they need to take him. They traced the call. Bobbi Morse and Alphonso Mackenzie entered a building, where a battle against HYDRA had just occurred. They found Coulson, surrendering to them and demanded to be brought to Gonzales.
- "We have a chance to hit HYDRA hard. They're operating on powered people. We can shut that down and save lives."
"Perhaps, but I'm gonna ask again – why should I trust you?"
"Because we all have our secrets. You have one sitting in the cargo hold of your ship, but I'm still willing to work with you."
- ―Phil Coulson and Robert Gonzales[src]
Phil Coulson offered to open the Toolbox if Robert Gonzales would support his attempt to attack a Arctic HYDRA Research Facility. Gonzales agreed as he only used his own team but put it up to a vote. With Bobbi Morse and Melinda May agreeing with the proposal Coulson had the majority.
Coulson succeeded in rescuing the Inhumans and having the base destroyed, but also secretly hacked in HYDRA`s computer to get information on the location of Loki`s Scepter and Wolfgang von Strucker. When he returned he kept his promise and opened the toolbox, yet he revealed Nick Fury was still alive and that he was in contact with Maria Hill. He sent the information to Hill who called in the Avengers who dealt a crippling defeat to HYDRA, killing List and arresting Strucker.
- "I tried to do it all alone, that was a mistake. Even Fury had a World Council watching over him, providing guidance."
"What are you suggesting?"
"One S.H.I.E.L.D. where I operate as director, under your advisement. This way, we'll have a cool underground base and a boat."
- ―Phil Coulson and Robert Gonzales[src]
With Ultron successfully defeated by the Avengers, Phil Coulson gathers Bobbi Morse, Melinda May, Robert Gonzales, and Gonzales' board aboard the Iliad, where Coulson finally revealed the true nature of Theta Protocol. Afterwards, Coulson proposed that the two factions unite as one S.H.I.E.L.D. Impressed by the fact that Coulson's secret plans had saved thousands of people, Gonzales accepted.
Phil Coulson was restored in his rightful position as director, with all of S.H.I.E.L.D. discovering that Nick Fury was still alive. Gonzales' council retained an important position, getting a similar role to Fury's World Security Council, although unlike Fury`s council they only had a role of giving advice. S.H.I.E.L.D.'s strength increased, now having various Quinjets, a Helicarrier, and an aircraft carrier.
- Captain America: The Winter Soldier
- Agents of S.H.I.E.L.D.: 2.01: Shadows
- Agents of S.H.I.E.L.D.: 2.15: One Door Closes
- Agents of S.H.I.E.L.D.: 1.22: Beginning of the End
- Agents of S.H.I.E.L.D.: 2.05: A Hen in the Wolf House
- Agents of S.H.I.E.L.D.: 2.07: The Writing on the Wall
- Agents of S.H.I.E.L.D.: 2.08: The Things We Bury
- Agents of S.H.I.E.L.D.: 2.10: What They Become
- Agents of S.H.I.E.L.D.: 2.14: Love in the Time of HYDRA
- Agents of S.H.I.E.L.D.: 2.16: Afterlife
- Agents of S.H.I.E.L.D.: 2.17: Melinda
- Agents of S.H.I.E.L.D.: 2.18: The Frenemy of My Enemy
- Agents of S.H.I.E.L.D.: 2.19: The Dirty Half Dozen
- Avengers: Age of Ultron
- Agents of S.H.I.E.L.D.: 2.20: Scars