After Scully left Nick's, Mulder walked to his car, threw the box she gave him in his car without really caring if the box kept its contents inside of it or if they spilled everywhere. He locked his car, and walked back inside the bar. He promised himself only one drink, but before he knew it he was drunk off his ass and taking a cab home. That's more or less the way things went for a few weeks after Scully left him. He'd go to work, drive straight to the bar and drink until he couldn't think of her anymore. The bad thing was, the more he drank, the more he thought of her.
One day, he felt he'd had enough, he needed to do something. All he wanted was to drive himself over to Scully's, get on his knees, beg for forgiveness and hope that she would take him back. But he knew, the closer she was to him, the closer she was to death. He would never forgive himself if she was killed because of him. So he did the next best thing, he needed to get away from D.C. for a while. He needed to get away from everything that reminded him of her, which was everything. He put out a request for an out of town assignment, and was surprised to learn Skinner had been looking for a deep undercover assignment for a while. He had not considered Mulder because he knew how hard it was for him to get away from the X Files.
Before he knew it, he was flying to Phoenix, Arizona.
Before he knew it, two years had gone by and he still couldn't get her out of his mind.
Xxx
Scully had been 5 months pregnant the first time she sought out Mulder. It had been a terrifying moment for her in which she thought she was losing the baby. One moment she had been fine, the next she was bleeding. She rushed to the hospital and everything checked out ok, but at that moment she knew he at least had to know. She called his office after a failed phone call attempt at his apartment in which the machine did not pick up. Two months later, a heavily pregnant and very emotional Scully tried to contact Mulder once more, but his cell phone and home phone were no longer in service. She had cried for an hour after, cursing herself and her hormones for the outburst.
The next day she phoned Skinner as a worried friend, only to learn that Mulder had gone undercover with no end date to his assignment. Scully knew these assignments were intense and it usually took years for people to resurface, if they ever did. She was lost, he was gone. She did not understand why he would take this type of assignment when all he could give her as an excuse for not wanting her was that the X Files came before anyone and everyone.
Two months later she gave birth with her mother by her side. She had a beautiful boy who she had named Samuel. Life went on. She kept her job at Quantico, adding a couple of classes to her repertoire and she was beginning to feel like she may be starting to get over Mulder. Not one day went by in which she did not think of him, of what he was doing at that very moment, and she'd pray that he was safe.
Life as a single mother was not easy, but she had enough support, work was understanding, and most important of all, she loved and enjoyed being a mother so much to even notice the hardships.