Clarke and Bellamy locate a supply bunker and find a bunch of guns in episode 1x08 "Day Trip".
The group investigates the crash site of the hijacked dropship in episode 1x10 "I Am Become Death".
The survivors from the ark set up camp in the remains of Alpha Station in episode 2x01 "The 48". From episode 2x02 "Inclement Weather". From episode 2x03 "Reapercussions". Appears in 15 more episodes.
Abigail goes to meet with Indra to try and negotiate a lighter sentence for Finn in episode 2x08 "Spacewalker".
Octavia leads people in a rescue attempt after the missile attack in episode 2x13 "Resurrection".
Clarke and Lexa hold their final war meeting before the assault near the base of Mount Weather in episode 2x15 "Blood Must Have Blood: Part 1".
Mulder spies on a military investigation into a crashed U.F.O in episode 1x10 "Fallen Angel".