As part of his plan to ensure his survival in the face of Sarath's imminent destruction, Monitor replaced terminally ill or injured patients in hospitals in Arkhaven with android duplicates of themselves when they were put into emergency stasis, perfectly imitating their templates and with all of the original's memories up to the point when they were created, while discreetly sending the dead originals to be incinerated as part of the rubbish. He did this to Susan when she attempted to put herself in a healing coma, resulting in the android Susan remaining in hospital and in contact with the First Doctor and Ian Chesterton while the original Susan escaped being incinerated when she regained consciousness just in time to climb out of the garbage chute she had been placed in.
Due to Susan and the android sharing brainwaves, they developed a subtle telepathic connection, occasionally experiencing flashes of what the other one was doing when they were asleep, although they were unaware that the other existed; the android didn't even know that she was artificial for a time.
The android Susan's nature was exposed when she was abducted by Church functionaries and was wounded/damaged in the subsequent attempt to rescue her. Having confirmed that she didn't know why she had been created, the Doctor and Ian took her with them as they searched for the original Susan and the still-missing Barbara Wright, who had fortunately discovered each other. The two groups were eventually reunited at the work camp where Susan and Barbara had been taken, the Doctor and Ian quickly explaining the android's existence to Susan.
When Monitor attempted to take control of his androids, the android Susan was able to resist his influence due to her connection to her template, allowing them to disrupt Monitor's control of his androids long enough for him to be destroyed, the same link saving Susan's duplicate when Monitor transmitted a signal to shut them all down. Although Monitor was able to damage the navigation computer of the ship that the evacuees were going to use to escape, the android Susan suggested that she could be connected up to the ship and pilot it based on her/Susan's memories of flying similar ships at an applied science moon camp. The android eventually broke down as the new society on Mirath was unable to repair her, but she accepted her fate, and was remembered by the colonists as "the Pilot". (PROSE: City at World's End)