This story is roughly set in season 6. It isn't really important for the story, but there are very mild spoilers for season 6, so I have hereby warned you. Enjoy.
"Cas?" Dean whispered into the darkness of the room. He thought he had heard the soft sound of wing beats. Maybe that was what had awakened him. He wasn't entirely sure though, mainly because he could hardly see a thing, it was so dark. He didn't want to turn on the light next to his bed either, so he wouldn't wake Sam, who was breathing evenly, soundly asleep in the second bed.
He was fairly certain, that it was Cas, who had just entered their room and not some big, bad, ugly monster, wanting to kill the brothers. Slowly his eyes adjusted to the darkness and he could make out the shape of a man standing by the window.
"Cas, goddammit, is that you?" he asked again, needing to hear that gruff voice, needing confirmation.
"Yes, Dean. It is me. I am sorry I woke you up. That was not my intention." the angel finally answered, somewhat cryptically. He turned around to face the window and looked outside, through a gap between the curtains, to survey the parking lot.
"Okay, well, it's too late for that now. What do you want anyway?" Dean asked, a little irritated and confused by this late night visit.
Cas didn't react to this at all. He just stood unmoving and continued staring out the window.
"Cas!" Dean said loudly, now becoming annoyed. At this Sam grunted in his sleep, turned over but didn't wake up. It was enough to remind Dean to keep his voice down, though. He was glad that Sammy slept again at all, now that he had his soul back. He didn't want to wake him up if he didn't have to. And being annoyed with an angel, because he didn't tell the brothers any more than he absolutely had to, wasn't a good enough reason.
"What the fuck are you doing here?" he asked again, more quietly.
Finally Cas turned around to face him from across the room. Even though Dean couldn't see his face in this kind of light, he felt the intense gaze of those blue angelic eyes on him and it made him a little uncomfortable.
He thought that it was a strange feeling, because Castiel would always stare at him and he had gotten used to it by now, it was normal for the angel. So why did it feel different now? He didn't have time to dwell on this question though. Cas started speaking and it interrupted Dean's train of thought, which might have led places he wouldn't want to go to.
"I am hiding." the angel explained his presence.
"Hiding from whom?" asked Dean, now completely focused on the problem at hand.
"Or what." Cas added, uncertain.
Dean realized the angel sounded scared and that scared Dean more than anything else could. He had seen Castiel facing death more than once without being the least afraid or worried, he had rebelled against heaven, against his own, very powerful, family and now he had the power of heavens weapons to back him up and he sounded scared. Something was very wrong.
"What do you mean, what?" Dean asked, now giving up on the idea of sleep for this night and sitting up in his bed.
"I don't know. I don't think it is an angel or anything like one, but it might have been sent by one." Cas explained.
"Sent by Raphael." Dean guessed and Cas nodded. "What a dick." Dean cursed quietly, but heartfelt.
"It might not have been him. It might be something entirely different." Castiel defended his brother, even though they were at war at the moment.
"Okay, but something is after you and you don't know what it is. Can't you just use your angel mojo and smite it or something?"
After all angels were the most powerful beings Dean had ever met.
"I haven't been able to do that yet. It is strong. I haven't actually seen the thing itself, just what it is capable of. I saw how it killed another angel. It is not easy to kill an angel, Dean." his voice faltered as he said this.
Dean only nodded. He knew this for a fact from his own experience.
Castiel slowly moved away from the window and sat down on the chair that was standing next to Dean's bed. Now that he was closer, Dean could tell that the angel looked exhausted. But he didn't have much time to study the familiar face, because Castiel bent forward to rest his elbows on his knees and then he hid his face in his hands. When before Dean had been uncomfortable feeling the angel stare at him, he was now disappointed that Cas was no longer looking at him and that he couldn't see the beautiful face anymore.
Wow, he had no idea where those thoughts had come from and he quickly blamed them on lack of sleep and shoved them into the deepest corner of his mind.
"Is there anything I… we can do to help you?" he asked softly, worried about Cas.
"I just need a break. If you let me sit here and rest for a while I will be fine. I will find a way to defeat whatever is hunting me." Castiel answered, slowly raising his head again to look at Dean.
"Okay, sure. Stay as long as you want."Anything that Castiel needed, Dean was willing to give. He couldn't bear seeing Cas so scared, almost broken. Hunted. That's what it was. His angel was hunted.
Wait, his angel? Where had that come from? He was still trying to work through the confusion this question had caused in his head, when he suddenly heard Castiel gasp as if he was in pain. At this, Dean jumped out of bed and knelt next to the angel, who was now holding his middle and almost doubling over from some kind of terrible pain.
"Cas, what's going on? Come on man, you gotta tell me or I can't help you." Now Dean was really scared, scared for Castiel. He had no idea what the hell was wrong with the angel or how to fix it. He just held Castiel's shoulders, trying to prevent him from falling off the chair.
"You can't help. It is close and looking for me." Cas suppressed a groan before he continued. "I don't know what exactly it is doing, but I can't risk it finding you and your brother."
"Wait, Cas, I don't understand. How is it hurting you, when it doesn't even know where exactly you are?" This whole thing made no sense whatsoever to Dean and he felt helpless watching Castiel cringing in pain and fear, caused by some unknown creature.
"I don't understand it, either." Castiel explained between labored breaths. "But I have to get as far away from it as I can. I will come back when I know more."
Castiel was getting ready to leave, Dean could tell. "Wait. I… What…" Dean didn't really know what he wanted to say. He just didn't like the thought of Cas being out there somewhere, on his own, hunted.
He didn't get the chance the figure out what he was going to say though, because apparently Cas was struck by another, more intense wave of pain. He unsuccessfully tried to stifle a cry and this time he would have fallen off the chair, if Dean hadn't steadied him.
"Okay, Cas, maybe you should lie down for a while." Dean suggested, trying to get the angel to move over to his now empty bed.
But Castiel shook his head. "I can't stay any longer." he gasped. "I will be better when I'm farther away from it."
Dean knew he was right, even though he didn't much like it. "Let us know if there is something we can help you with."
Castiel nodded in agreement and then vanished into thin air.
"What was that all about?" Sam asked quietly, after Castiel had left.
Dean almost jumped at the sound of his brother's voice. He hadn't noticed that Sammy was awake.
"How long have you been watching?" he asked wearily, instead of answering Sam's question.
"Long enough to know that something is wrong with Cas." Sam replied.
"Something is hunting Cas, but he doesn't know what it is, except that it's powerful." Dean started to explain the situation to his younger brother, who listened intently and looked very worried when Dean finished.
"And he said we can't help him right now?" Sam asked, thinking out loud. "Well, we'll see about that." And pulled his laptop closer and started searching for a monster that fit the description Dean had given him.
I plan to write at least one more chapter for this story, with a possibility of Destiel. Let me know what you think, please.