Area 51

Solution:
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Location of Bonus Rooms in order of how they appear in the game.
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X MARKS THE SHOT:
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To activate, shoot all the windows on the outside of Hanger 18.
Two windows can only be shot when the screen is scrolling to
the right, past the hanger.

TANK TOP:
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When you enter Hanger 18 shoot as many of the windows above
you to the right as you can. Later when you get on the fork lift, you
have to shoot the windows when it scrolls right. Then shoot any
window left seen. When the screen scrolls back left, point at the
remaining windows and shoot them when the screen completes scrolling.

HEAD QUARTERS:
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Shoot the three blue lights when the first missile guy is shooting at you.
One is in the upper left corner; the other two you shoot after you go
around the capsized truck. They are on the right side of the screen and
you can only shoot them when the screen is scrolling.
You get another chance after the Stat's screen when the screen scrolls
to the right.

CHOW PALACE:
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Just after you get the power up shoot all the windows along the far wall.
Shoot all the windows as you walk along to the right.

EGG CELLENT:
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While you are on the fork lift, shoot all the barrels (every last
one of them).

HEAD QUARTERS:
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When you are in the jeep at the first stop, shoot all the cockpits'
windshields on the F-15 planes. Shoot a total of 3. 
Then the windshield on the big C-5 plane.

EGG CELLENT:
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When you are in the first hallway in the ADMIT building. Shoot all three
ceiling lights and the EXIT sign.

HEAD QUARTERS:
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Shoot all two Picture Frames on the 1st and 2nd desktops. Then
shoot the two name plates on the doors of the offices including
the General's Office.

CHOW PALACE:
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Shoot all the paintings on the walls of the ADMIT building.
There is one in the 2nd General's Office.

EGG CELLENT:
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On the first screen in the control room, shoot all of the
computer screens. A total of 13 in all.

CHOW PALACE:
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When you get to the guys throwing barrels, shoot all the
stationary barrels.

GET A LIFE:
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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.