Takes place in Season 2 (spoilers for that) after Mike helped Coulson and Hunter escape.
Brigadier General Glenn Talbot of the United States Air Force was in his office thinking about the latest of his marriage counselling sessions with his wife Carla cursing the names Grant Ward and Agent 33 for making that to happen, not only that but he had a meeting with the Secretary of State Thaddeus Ross later in the week to worry about. Then a lieutenant came into his office and told him that his rival turned sort of ally Phil Coulson Director of SHIELD was on the line requesting him. "Now Coulson decides to call after missing my calls for some time..." Talbot muttered under his breath as he went to the phone and answered it.
"Coulson after I decide to start playing ball with you my calls after the incident at my base goes unanswered, what is going on there!" Talbot asked agitated the issues with his marriage and his coming meeting fuelling his anger. Talbot managed to take a deep breath as he listened to Coulson.
"Sorry General but it seems my group has been compromised again and I have only managed to figure out a way to contact you undetected but I don't think me and my team here have much time. This is going to sound weird but... I need your help in invading my base..."
It was sometime later in the Playground when Commander Robert Gonzales was watching a screen when being told there was a call being through and he answered it to see Coulson in a chair inside the Quinjet that he, Hunter and Mike Peterson had managed to take. "After Deathlok helped you and Hunter escape I didn't think you would be foolish enough to try calling this place Phil." Gonzales told him but Phil gave a slight chuckle.
"Well I called another ally and I thought i would call before I get my base back Robert." Coulson told him and Gonzales rolled his eyes. Just before Gonzales was about to ask why he thought he was getting his base back when there were an alarm sounded. Gonzales grew concerned when Agent Anne Weaver came in and said they were under attack, Gonzales looked to monitors and saw that the base was now swarmed with armed soldiers wearing uniforms of the United States Air Force.
Gonzales and Weaver tried to call their 'Real SHIELD' soldiers but then the room was now filled with soldiers forcing them to step back. "Oh here are my allies now." Coulson said as Hunter and Mike came into the room armed as well and Gonzales and Weaver looked like they were not afraid but dropped their calm exterior when they saw General Talbot walked into the office with a stern expression.
"Feels nice to have been able to storm a SHIELD base again, I would love to take control of it but I made a deal with my good friend Coulson there that he would be able to get his base back." Talbot told him and shook his head. "In that time since your Real SHIELD guys spent working against Coulson stopped me from offering assistance against HYDRA." Talbot remembering what Coulson and Hunter had told him.
There was some clean up after that, after regaining control of his base Coulson got his base back and worked something out with agents of the so called 'Real SHIELD' thought the ones who were willing to work with Coulson that is (Morse and Mack spent some time going over it before managing to come to an understanding and Calderon was not too fond but his decision to try and get the base back under 'Real SHIELD' by attacking Coulson and Talbot's men pretty much cost him the high seat of power and influence he enjoyed with Gonzales running the show). As part of their deal Coulson agreed to regular calls for updates and let Talbot put some of his men in Coulson's SHIELD so they could report back to them as sort of liaisons (so that there was not an incident where they would be compromised again and not be able to contact the military). As Coulson told his new support council of both members from his loyalists and of the 'Real SHIELD' it was a start to getting the military and government to trust SHIELD again, Talbot told him that there were the military officials that he saved from Garrett and his Deathlok soldiers who were vouching for him.
Of course they still had to deal with Grant Ward, needing to help the Avengers beat Ultron using the Theta Protocol, Hydra and battle against the Inhumans of Afterlife but things turned out pretty well. Eventually Gonzales managed to accept things how they were and he managed to find his place in this new SHIELD.
This was an idea I had for a long time and I actually thought this would be how the Real SHIELD storyline would end with Talbot helping Coulson gets his rightful position of SHIELD director back. I wish there were more stories of Talbot helping against them but the closest I could find was the beginning of a story called the Sniper and the Hacker and only then it was taking place after the Real SHIELD stuff. Seriously I admit the so called Real SHIELD had some good points but they did nothing but be total hypocrites (they hate Fury for keeping secrets yet they are more secretive than Coulson ever was with his SHIELD) and I doubt until near the end of the Season 2 that any of them did anything to fight against HYDRA (except for Mack and Morse who only did so when they were spying on Coulson and following his orders). Seriously I bet that if Gonzales had fully taken over that they would have crumbled. Seriously I wish they didn't bother with the Real SHIELD stuff and focused the second half of the season fighting against HYDRA, Cal and then maybe the Inhumans (seriously I thought that Cal or maybe Grant would be the main bad guy for the rest of the season, I think the season was better in the first half).