Well I've finally finished this story that I started months and months ago. It's been fun writing it! Thanks to everyone who has taken the time to read my story and thanks to everyone who reviewed it as well.
After the battle in the batcave between Clayface, Iron Man and Batman, things began sorting themselves out. Bruce had found Alfred in one of the upstairs living rooms unconscious, but otherwise healthy.
Together, Bruce and Tony took the frozen scattered remains of Clayface into the GCPD, where it was determined that he was still alive. He was frozen but tiny broken part of Clayface still had life in it. Clayface was taken back to a secure wing at Arkham Asylum where he was able to recover under intense and secure supervision.
The arrest bulletin for Batman was lifted as press reports filled out, recognizing the culprit as Basil Karlo.
Before Tony left Gotham to return to New York, he discussed more with Bruce and the two promised to seriously consider a business relationship between Wayne Enterprises and Stark Industries.
As for Pepper...
The hospital room was still white and boring. The building still smelled sickly. But everything seemed a bit clear to Pepper. The last time the doctor spoke to her, he said that she was on her way to recovery and would be fine, he just suggested resting and not working for the next several weeks until her strength was back.
She sat up in bed, her legs hanging off of the side. She felt the bandaged area where the bullet had pierced her skin. It hurt still. But the pain was becoming manageable. She thought of how lucky she was. Now not many people who take a bullet would consider themselves lucky, but Pepper did. She was shot with a high calibre rifle by one of America's most wanted villains, and she lived to tell the tale. There was still really only one thing on her mind though.
There was a knock at the door, startling her.
"Tony," she said, almost looking like she had seen a ghost.
Tony walked in, sunglasses on, a well-worn suit on and a heavy five o'clock shadow. In his hands with a bouqet of bright red flowers. He smiled when he saw her, he couldn't help it. He stood there in her hospital room for a second and the two kept looking at one another. Finally Tony spoke.
"You're still in bed? I was expecting to come back to a home cooked meal and to have all of my filing done."
Pepper threw one of her pillows at him, trying to hold back her laughter. They embraced in a hug. Something that Tony and Pepper hadn't done much before, considering they had such a public employer/ employee relationship.
"I heard all of these things, apparently some Clayman from Gotham City shot me? And they were saying that Iron Man went on a rampage looking for him, and that he and that Batman character captured him. Please don't tell me you went all the way to Gotham on some revenge trip," Pepper said with Tony's arms still around her. He didn't answer. But she did notice something. Tears were leaking down Tony's face.
"Tony... are you crying?"
He regained his composure quickly, "No, I'm just allergic to these flowers," he wiped away the water from his cheeks and threw the flowers on the bed next to Pepper.
They spent the rest of the afternoon in the room together, talking about everything that happened. Things felt normal again for the both of them as they both stood at the hospital room window, hand in hand, looking out at the New York City skyline. Blue skies, white fluffy clouds. And on a rooftop in the distance, a figure with the silhouette of a bat looked on and smiled.