- "Strucker and List have been running experiments on enhanced people. They've set up a base in the Arctic. I have a man on the inside who fed us their location."
"I can't trust you."
"Then trust the mission. Robert, don't let this be about you and me. The one thing we still have – both of us – is stopping HYDRA."
- ―Phil Coulson and Robert Gonzales[src]
S.H.I.E.L.D. agent Phil Coulson was permitted to put together a team to investigate the unusual and unknown. The team became complete with the addition of Skye. Grant Ward, however, was revealed to be a HYDRA undercover operative, even attempting to kill his teammates Leo Fitz and Jemma Simmons.
The HYDRA Uprising caused S.H.I.E.L.D. as an organization to collapse. Nick Fury commissioned Coulson to rebuild the organization from scratch, while Fury allowed the world to believe that he had died. Meanwhile, Robert Gonzales gave himself the same mission; however, instead of meeting with Coulson, he chose to attack his faction, causing a civil war. Ultimately, the two factions decided to unite to fight their common foe, HYDRA.
Simmons promised Ward that she would kill him when next they met.
HYDRA captured Deathlok and Lincoln Campbell during an assault. Deathlok was previously commissioned to find the scientist List and to bring him to justice; Coulson and Maria Hill knew that List knew of the whereabouts of the Scepter after its disappearance prior to the HYDRA Uprising.
Since Campbell was an Inhuman, Jiaying, their leader, was hesitant about freeing him, lest the whole species become discovered by Humans; however, Skye, another Inhuman, was convinced to try by Raina, an Inhuman with precognitive powers who explained that only Skye could save Campbell. Phil Coulson had a plan to assemble a small team that would infiltrate the base. The team would rescue the enhanced prisoners (Deathlok and Lincoln Campbell) and then disarm the missile defense system so that S.H.I.E.L.D. jets could bomb the facility. Robert Gonzales suggested they put the plan to a vote. Bobbi Morse and Gonzales agreed while Anne Weaver and Agent Oliver disagreed. Melinda May had the deciding vote but she wanted to talk with Coulson first. After their discussion, where May berated Coulson for his secrets and lies, she agreed with the plan. Simmons had a plan to place a Splinter Bomb on Ward during the mission to kill him.
Phil Coulson's team for the mission consisted of all the members of his old team: Grant Ward, Melinda May, Jemma Simmons, Leo Fitz, and Skye. The mission had two teams; Skye, Ward, and Simmons were rescue/medical, and the other team was Phil Coulson and Leo Fitz, who would break into the missile defenses and gather intelligence, while Melinda May would provide cover.
Doctor List and Sunil Bakshi were chatting about the prisoners' progress when a HYDRA operative entered and told them that they detected a plane. Bakshi realized it was S.H.I.E.L.D. so List ordered the operatives to shoot them from the sky. HYDRA then shot missiles at the Bus, destroying it. Coulson's team managed to escape the damage in a Quinjet.
They then broke into the base. When they got inside, they found Bakshi, who took down some guards. Bakshi asked Coulson if he could join Ward's team; Coulson agreed. Coulson then told everyone that they had only fifteen minutes before Robert Gonzales' jets arrived. Once Ward's team broke into the lab, the HYDRA operatives took List away. Skye then used her powers to take down the remaining operatives in the room. Jemma Simmons and Skye found Deathlok; Skye asked him where Lincoln Campbell was and he said he was in the other room but she had to hurry because he was in pretty bad shape. Skye took down the remaining operatives in the lab to rescue Campbell. When she reached Campbell, he was dead; she used her powers to start his heart again, saving his life.
While Grant Ward was looked for something to use to carry Deathlok, Simmons arrived from behind a wall carrying a Splinter Bomb. She went to throw when Bakshi stepped in the way. The bomb activated on his chest, disintegrating him.
Meanwhile, Coulson and his team took down the operatives in the mainframe room. Leo Fitz then started hacking into the system to disarm the missiles. Fitz was almost done disarming the missiles when Melinda May noticed Coulson was missing. She then found Coulson in another room on a computer gathering intelligence. She shot two operatives who were approaching and told him he was next if he did not come. May then contacted the Playground and told them they had the prisoners and were leaving HYDRA air space. Gonzales then ordered the jets to fire at the base.
- "Coulson, why didn't you just tell Gonzales why you really wanted to get onto the HYDRA base?"
"Believe it or not, he puts every decision to a vote. I know. And I was pretty sure if I'd been honest, I'd have lost the swing vote, so I did what I had to do."
"Last thing. Theta Protocol. Is it ready?"
"Yes, it is. Time to bring in the Avengers."
- ―Maria Hill and Phil Coulson[src]
Grant Ward called Coulson when he arrived back. Phil Coulson was surprised Ward did not join him but Ward told him he had to find an exit that would not land him in a cell. He told Coulson he returned Agent 33 to S.H.I.E.L.D. so she could receive forgiveness. Coulson told Ward he would try his best.
Leo Fitz and Jemma Simmons told Deathlok that they had to send him to a facility so he could get properly repaired. Robert Gonzales was happy because there were powered people on base. Gonzales told Bobbi Morse he planned on keeping Skye on base so he could learn how many Inhumans are out there. Coulson then gave Gonzales the Toolbox and told him to enjoy having it until Nick Fury wanted it back, revealing he was alive.
Coulson then took a call from Maria Hill. He did a video chat with her and revealed that he found the location of Loki's scepter. Coulson revealed to Hill that HYDRA probably did not know the Scepter killed him, but they probably know that it can control minds. He told her it was in Sokovia and that List was on his way there. Hill asked Coulson if Theta Protocol was ready and he said it was. Coulson then told her it was time to bring in the Avengers.
- Agents of S.H.I.E.L.D.: 2.17: Melinda
- Avengers: Age of Ultron
- Agents of S.H.I.E.L.D.: 1.01: Pilot
- Agents of S.H.I.E.L.D.: 1.02: 0-8-4
- Agents of S.H.I.E.L.D.: 1.16: End of the Beginning
- Agents of S.H.I.E.L.D.: 1.21: Ragtag
- Captain America: The Winter Soldier
- Agents of S.H.I.E.L.D.: 1.22: Beginning of the End
- Agents of S.H.I.E.L.D.: 2.18: The Frenemy of My Enemy
- Agents of S.H.I.E.L.D.: 2.14: Love in the Time of HYDRA
- Agents of S.H.I.E.L.D.: 2.06: A Fractured House
- Agents of S.H.I.E.L.D.: 2.19: The Dirty Half Dozen
- Agents of S.H.I.E.L.D.: 2.22: S.O.S. Part Two