S.H.I.E.L.D. Civil War

"This is not about Coulson. It's not about me. It's not about anyone on this ship. It's about S.H.I.E.L.D. We cannot afford to be enemies to each other when there are new threats out there waiting for the moment we are at our weakest. A house built on shifting sand will fall. And without a strong and united foundation, S.H.I.E.L.D. will fall again."

- Robert Gonzales to Melinda May

The S.H.I.E.L.D. Civil War was a conflict between the two factions of the peacekeeping organization S.H.I.E.L.D. after its downfall and subsequent reorganization during the HYDRA Uprising.

Background
"For a while there, it all went to hell. It was bad."

- Alphonso Mackenzie to Lance Hunter

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 the 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 didn't 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
"Secrets are what brought S.H.I.E.L.D. down the first time, and we won't let that happen again."

- Robert Gonzales

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.

Infiltration
Once Gonzales and his men found about 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, Agent Hunter, Coulson, and Melinda May became suspicious about Mackenzie and Morse. When Mackenzie couldn't explain to Hunter what he was doing, he knocked him unconscious and had him secretly brought aboard the Iliad. There he 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.

Open War
To be added

The Deal
Coulson offered to open the tool box if Gonzales support his attempt to attack a Hydra base in Antartica. Gonzales agreed as he only used his own team but put it up to a vote. With Morse and 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 Von Strucker. When he returned he kept his promise and opened the tool box, yet he revealed 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 and killed both List and Strucker.

Reunification
With Ultron successfully defeated by the Avengers, Coulson gathers Bobbi Morse, Melinda May, Robert Gonzales, and the other board at the Iliad, where Coulson finally revealed the true nature of Theta Protocol, which is secretly housing Helicarrier No. 64 so it can be used during emergency. Afterwards, Coulson propose that two S.H.I.E.L.D. faction 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.

Aftermath
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.