Well here goes. Just a little idea that popped into my head. And I'll confess to struggling with this.
Chances
Jake had had to learn how to stop others from seeing the chinks in his armour a long time ago. He could vaguely remember being continually compared with his well behaved, ridiculously intelligent brother. At school. At home. On Pandora. As a child he'd resented Tom for that, and it wasn't until Tom had metaphorically dragged him back into the real world after the injury that Jake realised something. It wasn't a particularly profound realisation, but it was there. Tom had hated the attention that was showered on him as much as Jake himself had. No wonder he was willing to risk having his head ripped off to go to a moon years away from their nagging parents. The scientific possibilities were just one big bonus (that had no doubt had Tom smiling that quietly self satisfied smile).
Maybe if it had been Tom driving his avatar, Neytiri wouldn't be screaming in agony. Somewhere deep inside he felt as though something was being torn from his soul. Guilt and fear made tears run down his cheeks as he paced back and forth waiting for Mo'at or someone to tell him what to do, what would end Neytiri's pain and bring their child crying into the world.
It had been several Pandoran years before the thought of a child had crossed either of their minds. Jake had to prove that the Sky Person within him wished no harm on the Na'vi, that he was fit to be leader of the Omaticaya, that he was worthy of Neytiri's love. It had taken years for the overt opposition to cease, for them to free enough to be ready to even consider the possibility.
The scientists had been cautious in their estimates of their chances of a pregnancy. The avatars had never been grown to become the sole house for a driver's soul, and the things that went along with that. They had never been created to ensure that they could successfully procreate with the Na'vi, and the combination of human and Na'vi DNA only complicated matters further. The scientists mentioned the infertility of mules and ligers, and said that without the equipment to run the necessary tests that they would assume the same for Jake. Jake could see in their eyes that they didn't want to tell him of the chances of a child being born alive that would be able to live a full life without complications.
Jake had been angry at first, if only to hide his disappointment. Neytiri had distanced herself from him for a time after that. He would see her every day talking to one of the elder Na'vi healers or her mother and she would never meet his eyes. He once saw her talking to Norman and looking surprisingly interested in whatever he had to say. Jake certainly wasn't jealous at the sight, which surprised him, just slightly bemused over what the retiring scientist would have to say that would interest an adventurous hunter and warrior.
He was five years, two months, seven days and some hours old when he almost choked on his midday meal. Neytiri had brought the subject up again, stating that if he, Jakesully, still felt himself ready then she wished to try. She had left him alone after that as he stared blankly at where she had been standing moments before.
That evening Mo'at requested his presence. It had been a strange conversation, being told all the worries Neytiri had expressed as well the determination that had crystallised within her. They could try, but the result would be for Eywa to decide.
Neytiri had become pregnant eleven months previously. By human standards she should have been dead for carrying so long overdue, but by Na'vi standards she was premature. Jake hoped it was the human genes speeding the gestation along its way, and so did everyone else. Jake shifted uncomfortably as a passing warrior's bared fangs and glare promised his death if anything were to happen to Neytiri.
It was in the early hours of the night when he was called to Neytiri's side. It was the smell that struck him first, so much more pungent despite the cleanup that had been done. Neytiri was in the deep sleep of exhaustion. Mo'at's face looked drawn and Jake found himself fearing the worst as she turned her gaze to him. He was startled to see her give him a small smile as she handed him what appeared to be a squirming bundle of cloth that he vaguely recognised as one of the healer's gifts to Neytiri on hearing the news of her pregnancy.
"Eywa has blessed you, Jakesully."
Jake was almost too scared to look down. But when he did he couldn't stop the grin that spread across his face.
"Four fingers!" Jake's grin turned to a look of wonder as a small hand reached out of the wrappings, grasping at the air.
"He is small but strong." Neytiri's voice was still a little weak, and it seemed to annoy her even as she shared a knowing smile with her mother.
"Let us hope he takes after his mother in all else. I shall not have my daughter's son be a fool." Mo'at stated as she cast a healer's eye over her daughter. She turned back to Jake as Neytiri gave a raspy laugh, giving him one last soul piercing look before giving a satisfied sniff.
Mo'at left them soon after that and Jake noted how strange it felt to sleep on the ground, near the roots of the Hometree rather than up in the branches. In the morning Neytiri would make the final decision on their son's name (Jake wanted to name him Tom for reasons he couldn't quite fathom, but Neytiri disagreed saying that a child needed their own name) and he would meet his new family, down to the last hyperactive Na'vi child and stubborn Dreamwalker.