What was that alone engineer doing in that big room of machine.
-> To take care of the physical parts perhaps. Who knows. Other engineers were outside thinking it was something nuclear. Certainly was weird.
---> Maybe he was the sys admin
-> This part pissed me off a bit. Reese seemed too cool about Finch hiding the fact he could have saved his lady love.
---> Reese already found out in Season 1 Ep 21. Finch later explained that her number came up at a time when they weren't working together and because of that nothing could have been done. I think he was apologising in this episode because Reese was in China on the laptop mission when Jessica tried calling and couldn't reach him.