Zion never quite knew what happened to Neo. It's not that they didn't try to find out, but they never could get into the machine city to find out. No matter how far Zion expanded or how many other cities popped up on the surface, the machines always held that corner of the earth, although they never tried to attacks the cities as an army again. There were never more than one or two sentinels attacking and the attacks were few and far between. Zion however, was never attacked again, probably because the cities on the surface were far easier to get at.

Hardly anyone stayed in Zion after it was attacked. Almost everyone went to the newer cities that were on the surface, as soon as they were given clearance. Some stayed behind though, to clean Zion up and live there. Some stayed for nostalgia, some thought it was safer, and others stayed thought it was their duty to restore the city that had kept them for so long.

Morpheus and Niobe stayed, along Councilor Hamann and a handful of others that they knew. They were given quarters on the same level as the Dock and every day they could see what destruction the machines had brought to their city.

After Zion had acchieved 'acceptable living conditions', so stated by the remaining Council members, Morpheus asked for a ship to try and go find the remains of the Logos. He was issued the Methusaleh - called that because she was made from parts salvaged from the old ships that were destroyed in the war - and set off as soon as humanly possble. With him went Niobe, Ghost, Link and Zee. They had picked up Link and Zee from the city that they were living in. Link had agreed to go and Zee, not willing to be parted with him again, came along as well. Now that the threat the machines posed was gone, anyone could ride a hovercraft.

After three days of searching, they found the Logos and Trinity's body within it. They also found Bane and could only guess what had become of his mind. When they got back to Zion, Trinity was issued a medal for 'outstanding bravery in the face of incredible danger' and was given a state funeral, at the urging of Morpheus. For days people passed by her coffin, wanting to see the face of the woman who had gone to the machine city with the One.

But they still didn't have the hero's body, Neo's body. Some people said that the machines had kept him and were studying him. Others said that he was in the machine city, alive, keeping the machines from attacking again. Still others said that he was in the matrix again, with his memory wiped, no idea of what he had done. Yet every story had something in common - Neo wasn't coming back.

And so, after many generations had passed, Trinity was just another heroine in a long forgotten battle, and Neo was just another statue in a park. But there were those who remembered. Those machines who remembered. And bided their time.