The Enterprise crew has to deal with a dangerous terrorist who has attacked Earth and is definitely not Khan (it’s totally Khan).
See also: Star Trek & Beyond.
Thomas Harewood is taking care of his daughter at the hospital when he is approached by Khan.
Scotty is drinking at a San Francisco bar when he gets a call from Kirk.
Kirk and Spock go to Starfleet HQ to discuss the incident with the volcano.
Source: The Worldwide Guide to Movie Locations
Thomas Harewood spots Khan across the street and then enters the archive to complete his mission.
Thomas Harewood enters the archive and is scanned through security.
Kirk enters the warp core to save the ship and receives a lethal dose of radiation.
Kirk and others examine the torpedoes that were loaded onto the ship. Filmed in the Switchyards area at the NIF.
Bowels of the Enterprise where, among other things, Chekov saves Scotty and Kirk when the gravity shifts.
Scotty works to hack the Vengeance's computers to let Kirk, Spock, and Khan enter the ship.
Spock beams to the surface and chases Khan through the panicking populace.
Spock chases Khan down and across a street.
Kirk gives a speech to the Academy to commemorate the lost crew members and to dedicate the new Enterprise.