As spoiler-free as possible:
Late in the game, Alfred will notify you that Lucius is not responding. Go to Wayne Tower to investigate.
*** Spoiler - click to reveal ***Your usual access point on the roof will be closed so you will have to enter through the basement. When in the main office, use the computer. At the end of everything, you'll have to use at the right time - when the attacker is pointing the gun at you, not at his hostage, but before he actually shoots you.