This takes place soon after The God Complex. I know he wasn't crying or anything, but, maybe he did later, off-screen, yeah? Anyways, enjoy!
River Song looked up from her book. A wheezing sound filled her tiny cell, and the empty corridor of her section of Stormcage. A smile graced her lips when the TARDIS appeared on the other side of the cell's bars. She closed the book, and left it on the bed in the corner of the room. Lightning flashed, illuminating the cell, everything temporarily bathed in a white glow. The doors to the TARDIS opened, and the bowtie wearing Time Lord emerged. The Doctor approached her cell, pulling his sonic screwdriver from the pocket of his tweed jacket. River stood up from the bed as he soniced the door, and a tiny click was audible, as the lock opened. River let the smile fall from her face when she saw the Doctor's face. His eyes were red, and there were tears glistening on his cheeks.
"Sweetie, what happened?" River inquired, concern flooding through her. The Doctor remained silent, but moved towards her, embracing her in a hug. She returned the gesture, squeezing the Time Lord slightly. She rested her head on his chest, and she could hear his hearts, that familiar double beat. River felt the trembling in his limbs, and she lifted her head, rubbing the Doctor's arm, trying to soothe him.
"My love, what's wrong?" River said gently. The Doctor pulled away from her, looking sadly at her. He took a deep breath, trying to regain his composure.
"I… I left them River," the Doctor's voice trembled as he spoke. "Amy and Rory. I left them. I destroyed Amy's faith in me, and I abandoned her. Again. I'm all alone." River met his eyes, sympathy in her own. She took his hand in hers, and led him over to the bed, moving the book to the dresser next to them. River gently pressed down on the Doctor's shoulders, trying to make him sit down on the bed. He complied, hunching his shoulders, and looking down at the cell floor. Lightning flooded the cell again, as River sat next to him. She put an arm around him, and drew him close to her. The Time Lord buried his face in her hair, the trembling fading from him.
The two sat in silence for a few minutes. River stroked the Doctor's hair, while she held him close. The Doctor mumbled something, breaking the silence, but whatever he said was lost in her hair. River looked down at him, confusion etched on her face.
"Sorry, what was that sweetie?"
The Doctor raised his head. "Can I stay with you? Just for tonight. I don't want to be alone." His eyes met River's, and she could see the sadness and wisdom that shone in their depths. She smiled at him.
"Of course you can sweetie."
The Doctor never failed to amaze River. The Time Lord could face anything in the universe – he's proved that time and time again, yet, he is shattered to pieces by leaving his companions, even if it is to save them. He is terrified of himself. Afraid of hurting those around him, but also afraid of travelling the stars alone. Despite all of his friends' protests that they wouldn't change the fact that they had ever met him. River looked down at the mad, impossible man leaning against her. He had closed his eyes, his breathing the only audible sound in the cell.
The Doctor shifted, and River realized he was sleeping, as he emitted a soft snore. River gently laid him down on the bed, glad he was asleep. She drew the thin, green, prison issue blanket over him, pulling it up to his shoulders. She lay back on the bed, beside the Doctor. The Time Lord rested between the wall and River. River was amazed, every time, at how young he looked when he was asleep. How vulnerable he really was. He tried so hard to be strong for those that looked up to him. He was so young, but so old.
Lightning flashed again, accompanied by thunder. River looked to the Doctor, hoping it would not wake him. It didn't seem to bother him, so she rolled over to face him. Her eyes slipped shut. The Doctor's breathing calmed River, making her drowsy. Another smile graced her lips, and she drifted to sleep, dreaming of her past, and his future.