One faction down, another to go. Following Rockets' Red Glare, speak to Desdemona to trigger this quest. She will direct you to teleport to The Institute and head for the relay control room, the same room you first accessed during the Mass Fusion quest.
After speaking with Z1-14, kill everyone else in the room. Z1-14 will man the room's controls and teleport members of The Railroad, including Desdemona. After speaking with her, head to the reactor as indicated by the waypoint. Unsurprisingly, The Institute has locked down the Advanced Systems lab entrance leading to the reactor.
Take a detour up to Father's room and access the nearby terminal to override the lockdown. When you've finally made it inside the Advanced Systems lab, head toward the reactor chamber. Reach the reactor and activate it. Tinker Tom will teleport you back to the relay room, after which you'll need to speak with Desdemona and rescue the Synth version of Shaun. Step into the relay once more. Activate the detonator to finish off The Institute, then speak with Desdemona to complete the quest.