The weeks which followed we dull and repetitive for Sophia, although she did her best not to let Khan know in case he worried. He visited her most days. Sophia was fascinated by every advance in everything. She pestered him for information about the Federation most of the time, although she had enough tact to avoid Starfleet. Khan spent most of his time working but he didn't seem in the least tired. She did worry that the security guards were hurting him more often than ever.
One day Khan came in looking smug. His face never showed much emotion but she could tell what he felt. "I know that you are bored here. I've talked to the Admiral and he has agreed that you can be my assistant."
"You mean I actually get to do something?" She grinned. A flicker of amusement crossed Khan's face.
Several days later Sophia started working with Khan. There were a few odd looks from the team of people working for Khan but they knew by then not to ask. At the beginning Sophia spent most of her time organising what was going on. She found that there wasn't much logic to the order they were working on the ship which was to be dubbed the USS Vengeance. She didn't voice her distaste at the name. As time went on she started to work on designing the ship itself. She would have enjoyed it if she hadn't known about Marcus' plan to start a war with the Klingons.
The longer she worked with Khan the more she suspected that he was up to something. He was always last to finish in the evening and first in in the mornings. When she asked him what he was doing he claimed it was something she knew it wasn't. A couple of times she had caught him flicking to a different document but he never told her what it was. Sophia was worried that he was working on something to save his crew but didn't trust her enough to tell her.
About year after being woken up Khan disappeared. Sophia got to his office and found Marcus and several security guards waiting there. She was immediately taken back down to a cell. An hour later Marcus came down. "Where is he?" Sophia shrugged. "If you don't want trouble you will answer my questions."
"I don't know where he is."
For the next few days she was locked in the cell. No-one gave her food or water or paid any attention to her. By the time Marcus came back she was exhausted and weak. She did her best to sit up but even that was too much of a strain. A hand supported her head and a glass was pressed to her lips. She drank gratefully. It took her a long time to realise that Marcus was the one helping her. "Where is he?" The Admiral asked very softly.
"I don't know." She rasped. "He wouldn't tell me anything."
Marcus bent down so his face was close to hers. "Do you know anything which might be useful?" He asked. She shook her head. Sophia closed her eyes.