Secret 1: Up there
When you drop down the air vent early on in the level, you are left in a control room with a chair that has some dots on it.
There are two rooms that open up on the side of the room, one has a teleport, and one does not. Go over to the one that does not have the teleport, and turn on your jetpack, and fly straight up. You will eventually see a small alcove with an Atomic Health. Go in there to get the health to get the first secret.
Secret 2: Hidden computer bank
When you are in the computer area under the main entrance room, you will see a strange symbol on the wall.
If you jump up there, it will lower one of the computer banks in the next room, revealing a secret area that contains an Atomic Health. A sound will play to indicate that the door has opened that is just behind the wall on the right. Go in there to get the secret. Once you go in here, the door will close behind you.
Secret 3: Behind the Holoduke
In the same room where Secret #2 was, you will see a Holoduke on top of a computer bank. The wall behind the Holoduke is a secret one. Open it up to reveal some steroids. Go in there to get them, and you will get the third secret of this level.
Secret 4: Computer box
The fourth secret is in the room with all the boxes. In one corner is a computer. If you "use" the computer tower (not the monitor) one of the boxes in the room will open, revealing some scuba gear and armor. Go in there to get the gear and the secret.
Secret 5: Crack in the wall
The fifth secret is right next to the fourth. To the left of the computer from the last secret is a crack in the wall. Blow it up. Go in the newly opened area to get the fifth secret of the level.
Secret 6: Bridge to the RPG
The fifth secret contains the way to the sixth secret. Once you are inside the room from the last secret, make your way to the back, you will see a red handprint on a very dark wall. Using this hand will open up a teleport right to the left.
Going through the teleport will put you next to a bridge, which looks very familiar from the kinds of bridges you saw in Episode 1's "The Abyss" level. Crossing the bridge you will see an RPG. Go get it for the sixth secret. From here it's advisable to retrace your steps and not just jump down, or you will have to re-follow a decent sized part of the level to get back to the room of boxes.
Secret 7: Inside the spaceship
Shortly after the room of boxes, you will pass a short conveyor. Let yourself get picked up by the crane, and when it drops you off, you will be in a small computer room with a switch. Flip the switch.
At the end of the corridor behind the red electrical charge shown here will be a teleport that has just opened up. Take it and you will be left in an EXTREMELY SMALL room, with nothing but a switch. Flip the switch, and a door will be opened to the inside of the UFO. Go in here to get the seventh secret, as well as the Atomic health that is in here.
Although widely reported as an official secret, developer Allen Blum confirmed in September of 2008 that the game does not count this as a secret.
When you first get inside the blue Access Card door, there is a computer on a desk in the small alcove right next to the door. If you use this computer (it doesn't matter if it has been blown up or not), it will open a door on the far side of the room. Run over there, and a timed door will have opened with a medkit inside.
- Near the end of the level, a monitor shows a giant flying saucer firing upon a city, namely at the Dukeburger building. There is also a shielded flying saucer in a hangar with a bottle standing on it. Both scenes are an homage to the film Independence Day.
- This requires the DNCLIP code, as you can't fly over the fence legit. The jeep waiting in front of the fence has "3D Realms Prop. Dept. #4330 Jeep" written at the back of the jeep. The 4330 is a reference to the texture used, and the message as a whole is a reference to a blooper from the Independence Day movie.
- The bus standing outside Area 51 has "ILUVET" for number plate, referring to Spielberg's E.T. the Extra-Terrestial movie.
- Groom Lake is where the real life Area 51 is established, except that it's dried-up. There's a clearly visible UFO under water here, which can even be destroyed.
- In the crate room, there is a box that has "Received from Roswell, N.M., 7/2/47, to W.P.A.F.B, OH Hanger 18" - W.P.A.F.B refers to "Wright-Patterson Air Force Base" situated in Ohio. This references the conspiracy rumor that wreckage from the alleged 1947 UFO crash in Roswell, New Mexico was transported to the base and stored in Hangar 18. Seemingly the wreckage has appropriately been moved to Area 51 instead.
- The alien ship in the hangar port is the small interceptor ship from the film Independence Day. Accessing a secret area, you can enter the interceptor, where you can even see the nuclear missile used in the climax of the film. The wine bottle on the ship is a deliberate flaw, as there are no soda cans in Duke Nukem 3D.