The Son brings the baby and helps activate the portal to send his family home but before they can depart the Runaways arrive with their new inhibitor weapons in episode 3x04 "Rite of Thunder".
First Bones sneaks Kirk onto the Enterprise and later Kirk and Scotty teleport aboard and get captured.
Bowels of the Enterprise where, among other things, Chekov saves Scotty and Kirk when the gravity shifts.
Source: The Worldwide Guide to Movie Locations
From episode 3x06 "Formicida".