The room you're describing sounds like the location of scene 3, not scene 2. Once Emma gets the ability to leave the hideout and walk around the city, there are a couple of different missions that have to be done before the prison break (where you fight Jaeger and end up rescuing Selene) can be attempted. One of these missions is done by Emma and Lex, to the east, and one is done by Emma and Jamie, to the northwest, the one where Jamie disguises herself as Starlight and disguises Emma as her sidekick. This latter mission is the one where scene 2 can be unlocked; near the beginning of the mission, while Jamie is distracting the guards. The location of the mission is around a corner from where you can find a reporter discussing the exploding apartment.