I have a question regarding the story. In Chapter 2:
"I…heard that Shinji is now living with you vice-commander." She said.
"That's correct," Burke replied. "It's been only a week, and there are still some things to work out, but I would like to think it's going fine so far."
"I see," Misato said followed by a pause. "How is he being monitored?"
"Intelligence has eyes on him," Burke answered. "He can leave my apartment when he wishes, I made sure to tell him that. I even showed him a convenience store within walking distance. So far, he hasn't gone anywhere on his own volition."
"That might be for the best. Could it be that you're giving him too much leeway?" Misato asked. Burke titled his head in confusion as he processed her question.
"I… don't understand your question Captain," Burke replied. "He's not using much of the leeway he has already. He can't leave the city by himself if that's what you mean, and if you think he could be recaptured by Nerv, they would have to stage a full scale attack on the city, unless you believe a Mark 04 can disguise itself as a janitor or something."
"What about being able to have access the Eva Units?" she asked. Burke's face was beginning to develop a scowl.
"Not possible," he replied. "Unless he has direct permission from either myself or the Commander, he can't enter the facility to use the men's room, let alone go to the Eva cages."
"We need to take every precaution-" Misato began to say before getting cut off by Burke.
"And speaking of precautions, I do have some questions regarding the ones you took."
"Questions?" she asked.
"During our interrogations, Shinji talked about the few hours that he spent aboard the Wunder. Let's just say he didn't paint too rosy of a picture of his encounter with bridge crew." The two men could tell she had gritted his teeth.
"There were circumstances beyond our control," as all she said.
"Circumstances you say? You had him brought to the bridge when he was still unable to know which way was up," Burke countered. "Why would you do something like that? Couldn't you have gone to where he was under lockdown?"
"We had to confirm if it was really him," Misato argued. "I was in no position to leave the bridge. We did have the Nemesis series after all."
"I more than understand that you and the crew were under tremendous strain during that battle, but I have been going through your report and the ship's log, and I found that the attack didn't happen until after he was brought to the bridge. So I'm asking again, why was he brought onto the bridge? Why couldn't it wait until the ship was relatively safe?" Misato took a breath before she answered him.
"The bridge was the safest place on the ship to calibrate the DSS System. And as I stated earlier, there was no solid confirmation that he is Shinji Ikari. I felt that it wasn't necessary for me to leave the bridge at that time." Burke didn't buy it, but he decided to let it side She was right that precautions needed to be made at that point. But as it is now certain that this is Shinji, he still couldn't get her reasoning.
"They wouldn't admit this to you willingly," Burke began as he sat himself back up. "But I have been approached by several senior staff members as well as some city officials asking that we put a DSS system on him. After some prodding, they admitted that it was the Captain who brought it up with them."
If Misato did indeed confirm it was Shinji and not an Ikari-Type on the Wunder's bridge, why did they put the DSS system on him to begin with? Also, why did she insist on trying to have him fitted with it once he was in the city, when they should have confirmed by then that it was really him? It is very clear that she knows it is in fact Shinji, and still expresses concern for his well being - so why?