Here's the second part. Just be warned, I find it significantly harder to write from Smith's POV, which may or may not be reflected in the quality of this chapter.

It made no sense.

It had been an action without thought, and yet the memory of it still plagued him with its impossibility. He would have been willing to call his actions reflexive, except that, unlike a human, he had greater control over such things. He would not have reached out and caught a falling virus, consciously or otherwise.

He knew this one, though. There was that. She was one of the rebels, one of those who still blindly searched for the One. He'd pursued her many times before, and each time she had managed to evade him. He did not believe in such things, but this one had fortune on her side, clearly.

But, more than that, he knew her name. She was always his chase, his hunt. He knew how fast she could run, how she reacted if cornered. Not that it signified. She meant nothing to him, named or otherwise. She was just another threat, like all the rest. Something else to be eradicated from the system by any means necessary.

So why had he saved her?

It went against his programming, which in itself was a frightening concept. If he continued to display such aberrant behaviour, he would be recalled to the Source, to either be reprogrammed or deleted.

I should have left her to die.

Not that that mattered, either. There were countless others like him throughout the Matrix, and, doubtless, another would be created to take his place.

In his mind's eye, he saw a flash of her eyes, wide-open and afraid. How she'd trembled when he set her back on her feet. How badly he'd just wanted to turn away, to walk away and leave her now that he's already done the impossible.

But he didn't.

Something had compelled him to remain where he was, to watch her run away without a backward glance.

Until, that is, she did look back. Even from that distance, he'd felt her eyes on his face. Searching, curious now, rather than afraid.

He'd heard her words of gratitude, almost inaudible on the wind.

He'd wanted to forget the entire incident. But he could not. It was a part of his memory now, written into him as irrevocably as the rest of his code.

A flaw, a glitch, a malfunction.

Another threat to be erased.

He would return to the Source willingly, he decided. Remove this… mutation from his mind before it could spread any further.

But first, Smith thought, he would find this human again.

And what will go down when these two meet again...? To be honest, I've no idea, I haven't got that far yet. What would you like to see happen? Suggestions are always welcome!