Disclaimer: I own next to nothing. If you recognize it, it's not mine.
The war was not over, not truly. Peace had come to Zion, the people rejoiced, but an air of suspicion still lingered. A cold war. A standstill. The machines had not attacked, would not so far as everyone knew, but after 100 years of war, peace is not so easily understood or accepted, by either party. And so while some lived in a sort of optimistic ignorance, others prepared and patiently waited for the other shoe to drop, for the peace to end and give way to the pain and misery, the hope and despair, that the people of Zion had always known.
For nearly a month following the sudden withdrawal of the machines from Zion nothing was known of the savior's fate. Though the people, even the initial disbelievers, quickly acknowledged that the only possible explanation for the new found peace must be that Neo was in fact the One and had fulfilled the prophecy, with no word it could not be known just what had happened. Most feared he was dead, and Trinity as well since she had accompanied him to the Machine City. The shock, then, when both returned one day to Zion, was overwhelming. To most they gave no details, saying only that they did what needed to be done. Even the Council received only bits and pieces of the truth. Yes, they made it to the machine city, just as Neo was instructed to do. Yes, he was able to convince the machines that the rogue agent program was a far greater threat than the people of Zion. And yes, he entered the Matrix and defeated Agent Smith. How did he survive? How were the two able to return? They said only that the machines showed their gratitude by enabling them to do so.
To their family they said more. Those closest to the couple could see through their simple explanations and knew there was more to their journey. Trinity had died. Neo had died. Yet somehow they were here, complete, seemingly unharmed. Neo had been blinded by a possessed Bane before ever reaching the city, but his eyes were fine, his face showed no signs of any burns. Nor did Trinity have any scars from the pieces of metal that impaled her body, killing her. How that was possible no one knew. They both woke on the ship, breathed; alive. Confused, but alive. The ship had been repaired, seemed to be in just as pristine a condition as their bodies were. And so they returned home to Zion.
Their miraculous return meant different things to different people. Some thought their survival was merely a gift, a gesture of goodwill from the machines following the destruction of the Smith program threat. Others thought the One needed to return, to protect them further, to save them from some mysterious tragedy the future held. Perhaps the prophecy had not been fulfilled as they all had thought. Perhaps his tour of duty had not yet reached its end. Whatever the reason, they felt he was undoubtedly still needed. But there were others who believed neither of these things, the suspicious ones who thought it must be a trick. They had after all died, and even those who were not made aware of that fact hesitated to believe that anyone could survive a trip to the Machine City. If they were reinstated, so to speak, by the machines, then it must have been for some reason. The system, after all, knows better than anyone or anything that without reason and purpose a thing, a person, need not exist. Were they spies of some sort? Were they sent to keep an eye on humanity, to ensure that the balance remain, that people don't get out of hand, too cocky, too eager to complete what they felt was their mission, to destroy the Matrix? And so while Neo was seen by some to be the One, their savior, bringer of peace, others doubted he still had humanity's best interest at heart.
Truly Zion had changed, just as one would expect it to. Fear and doubt can not be so easily abandoned and though they were no longer at war, the people of Zion struggled with peace. There could be no Utopia. Conflicts arose, even in the first year of newfound peace. Some related to the desire to expand Zion, to try and build new cities, create a new world. This of course would require additional machine power, which excited some and frightened others. Factions rose among those who worked to free people from the Matrix. There were those who worried peace may not last and all those they could free should be unplugged as soon as possible. Others acknowledged that it took time for many people to come to terms with the reality of reality, and therefore patience was called for. Many people wanted to change the political system, alter or perhaps even do away with the Council all together. These, of course, were the extremists, the fringe, just as those who plotted against the One, viewing the man who returned as a threat. But they existed none the less and brought with them potential peril.
Though it was not seen necessarily as a dangerous place, Zion was no longer the safe haven, the home sweet home that so many had felt it was during the war. It was a new place. Peace heralded a new beginning. And this is why they chose the name Nysa, because she was the first to be both conceived and born into this new world, a child who signaled a new beginning.