The Oracle cryptically told some Resistance members about her by saying "and the child would be hope" and there was an assumption she was gifted or aware.
Perhaps the Agents didn't want her to be found, and the orphanage was burnt. The next day, Eight Ball went to the deserted orphanage to find her but he was killed by fire, not listening to Charon's warnings. Soon after, Link made the attempt and realized that the tag was on a man instead. He followed him on the roof while chased by Agents.
Link saved her, by riding a phone line to the ground and eventually rescued her from the Matrix.
The next day they introduced her to the hovercraft's captain who came from Zion.