How did this Happen?

Summary: It's been a few months after the Battle of Manhattan and the avengers are now moving in to the newly built avenger tower along with Phil Coulson. What changes are in store for them now that they are under the same roof? And why does Coulson look so angry?

Warning: There will be cursing, and violence. Also there will be some OOC moments.

Pairing: Main- Tony/Phil, Beginning pepper/tony

Disclaimer: I do not own The Avengers.

Chapter 1:

The past few days after the battle had been intense. Everywhere you looked there was evidence of the battle. Regardless of the fact that they had saved lives that day the avengers couldn't help but cringe every time they were greeted with the sight of it. Everyone had volunteered to help with the clean up eager to reverse the damage they had done but Nick Fury had calmly stated that they had done enough and that they had Shield workers aiding with the clean-up. So there they all sat in the conference room on the shield helicopter waiting to find out why Fury had dragged them there. Fury for his part looked distinctly uncomfortable as he stood before them and that made them edgy. Whatever they were expecting though it wasn't what they had heard.

"Phil Coulson is alive"

The team sat in complete silence digesting this information before chaos erupted.

Clint and Natasha were furious. They had known Coulson the longest and were devastated by his loss and they made sure Fury knew that they were pissed.

"How dare you lie to us? You know how much it hurt to hear that he had died you heartless bastard!" Hissed Natasha dangerously as her hand itched to grab one of the many knives she carried.

Clint wasn't fairing to well either. "Do you KNOW how guilty I felt knowing that I had a hand in his death. That if I had not been controlled by that glow stick wielding bastard I might have been able to save him all to find out that he was alive the whole time!"

Fury had opened his mouth to explain but was cut off by Steve who was terribly upset himself. "You had his trading cards! You used them to guilt us into fighting. I felt terrible knowing that I couldn't even spare a minute to sign them for him. You lied to us!"

Thor was shaking with rage as he bellowed out. "The sight of him being stabbed was the last memory I have of him as I was trapped in that blasted cage. That image has haunted me knowing that had I not fallen for Loki's trap he might have survived!"

Bruce had not yet spoken as he was too busy trying to control his other side. Another lie, another betrayal he thought to himself.

In the midst of all this chaos nobody noticed a silent figure slip out of the room. Tony had many thoughts running through his head as he made his way to the hospital unit.

He's alive…I can't believe Fury lie- actually no never mind I can believe that, fucking lying bastard…

As he neared the hospital unit he quietly slipped inside. He slipped down the hallway silently as he glanced into each room. Finally, he came to the last room at the end of the hallway. He glanced in and saw Coulson propped up on a pillow reading what looked like a history book focusing on Captain America.

Ever the fan boy, hmm I will have to get him a new set of trading cards as a get well gift. Maybe I can't even get capsicle to sign them…

He knocked on the door lightly effectively getting the agent's attention. Coulson did a double take as he looked over to see who had knocked. Though his emotions were mostly masked tony could see a hint of confusion in his gaze as Tony grabbed a chair and dragged it over by Coulson's bed.

"Agent."

"Mr. Stark."

They greeted each other neutrally before there was silence. The silence dragged on for another minute before Coulson gave a wary sigh. He opened his mouth to speak but was cut off by Tony.

"I'm sorry…" Tony said quietly watching as Coulson's eyes widened in response. It was a well known fact that Tony rarely ever apologized. Those wide eyes then narrowed in suspicion wondering why Stark was apologizing and debating in whether or not he really wanted to know.

Finally curiosity got the better of him, "What are you apologizing for Mr. Stark?"

Tony sighed and looked away a hint a guilt showing on his face before he turned to look the agent in the eye. "After Cap and I got done fixing the engine Fury made an announcement. Said the doctors called it, that you were dead. It caught me off guard and I said a few things about you that I really regret, so I am sorry."

Coulson scrutinized him for a few seconds but found nothing but sincerity on his face.

"Apology accepted Mr. Stark." He said with a nod.

Tony nodded and soon began filling Coulson in on what all took place during the battle, including Fury's speech and what he used to help motivate them. Needless to say Coulson was furious when he heard that Fury had ruined his near mint vintage Captain America trading cards. His anger quickly faded though when Tony accidentally let it slip that he was going to buy him a new vintage set and have the good captain sign them. Coulson's eyes widened when he heard that, and he couldn't keep the smile off his face when those words sunk in.

Tony had visited him a few more times after that while he stayed in the hospital sometimes bringing his teammates or pepper along, but mostly he came by himself. When the day came that he was finally being discharged from the hospital Tony had come barreling in telling him that he was now living at the Stark tower, no exceptions.

Coulson had tried to refuse but when Stark is determined that is no getting through to him so Coulson grabbed his bags and left for the tower.

-Line Break-

It had been two weeks ago since Coulson moved into the tower, and since then everyone was getting along fairly well. Steve and Tony even seemed to slowly be becoming friends. It was definitely a work in progress but at least now they were civil towards each other.

Coulson stood and watched as Tony, Pepper, and Steve talked amongst themselves. It seemed like they were having a calm discussing before Tony suddenly clapped his hands in excitement.

"Hey agent would you mind getting the others for me and bring them here?" Tony shouted from where he was standing. Coulson just nodded and turned to go get the others but not before seeing Tony give Pepper a kiss before running out to go down into his lab.

Five minutes was all it took to locate the other 4. They had just stepped out of the elevator when they came upon a horrifying sight.

There in the middle of the room stood Pepper and Steve in a tight lip lock. Coulson could feel his blood start to boil as the others let an out a startles gasps which caught the lip locked couples attention. They looked at the rest of the team and Coulson with wide guilty eyes.

Coulson was about to curse them out, to ask him what the hell they thought they were doing but he froze when he heard a strangled gasp from across the room. Everyone whipped their head around and saw a clearly distraught Tony standing there.

"P…Pepper?"

A/N: An that's it for this chapter. Hope to get the next chapter out sometime next weekend but we shall see. Anyway hope you like the story so far! Reviews are always welcomed!"