When the under ground explosive room appears, shoot all visible explosives.

Here are some hints on getting into just a couple of the seven secret rooms
hidden in Area 51. There are fourteen separate secret rooms entries...

In the Hangar (Wave 2), shoot out the three blue "emergency" lights during
the
first lockdown. There is one to the left and two to the right of the red
tractor truck.
You have to get the one on the left during the quick camera pan. This will
get you
into a room where aliens are taking a latrine break. There are 36 items to
shoot in
this room; six of them are aliens.
You can score over 40,000 points by hitting everything - a major scoring
opportunity!
This entrance to "Head Quarters" is secret room entrance #3.

By shooting all 15 windows in the back of the hanger, players can get into
the secret
room entrance #4, "Chow Palace." This will open up into a huge power-up
feast, with
21 icons: two give shotguns; two give machine guns, and 17 give grenades.
This room
is also the only place in the game where you can see a Stage 2 alien, the
intermediate
bioform between the Stage 1 zombies and the full-blown Stage 3 Kronomorph
alien.
Here the Stage 2 is happily munching on a poor human.

When you get into the Admin Building (Wave 4), shoot out the first "exit"
sign and the
first three ceiling lights right around it. This will get you into a room
where there are
disturbingly cute alien babies hidden insi de eggs. You can score over
15,000 points
in this room. This is secret room entrance #9.