Duke Burger has four secrets. These are the areas that are recognized as secrets by the game. There are a few other areas that are not recognized by the game as secrets. This secrets area will only show the "true" secrets in the level.
Secret #1: Hidden Bypass Room
The first secret is in a room that is above the drive through window. The way to it is far easier with a jetpack. Looking at the shot below, you can fly into the wall (again, "X Marks the spot"). You can get up there without a jetpack if you happen to have not blown up the barrel in the street. Standing on that, use steroids, and then run at the spot, and you will get in that way too. Again, MUCH easier with a jetpack.
Doing so will reveal a hidden room with several bits of ammo and health. Go in here for the first secret of the level. You can get out of the room the way you came in, but if you go through the small area on the other side of the room, you will come out behind the forcefield in the kitchen area. That will bypass the need for the blue key, and the entire shrinker move in the bathroom, although the doors to the restaurant will still be locked.
Alternatively, if you just want the weapons and don't want to use it as a bypass, you can get to it from inside the restaurant by going into the kitchen area, using the steroids, and taking a running jump from the counter straight at the wall.
Secret #2: Desk Switch
When you are in the back office room of Duke-Burger, you will see a switch on the desk that is here. Flip the switch, and it will temporarily open up a door at the top of the crates in this room.
Once you flip the switch, run out and jump up into the area now accessible at the top of the crates. You will collect a freezer weapon, and the second secret by going up here.
Secret #3: Rotating RPG Door
The third secret is in the room with the poster of the dog anatomy at the end of the underground conveyor system. There is a light switch right next to the drop off to the conveyor. If you flip that switch, the wall will rotate. There is a hidden room behind here you can get to. Be careful though, it's quite easy to get squished going back here.
A room will be revealed with an RPG on a shelf. Go in here to collect the third secret. A word of warning, getting out of this level is even harder than getting in, actually.
Secret #4: Scrappy Due
The fourth secret is in kennel area. If you go to the side of the kennel with the Scrappy Due puppy, you will need to blow off the doors to the kennels with a pipebomb (if you do it right, you will not blow up the puppy). You will need to make your way unto the upper left of the four specific cells. The back wall is a secret one. Open it up to reveal the fourth secret and some pipebombs.
- The rotating sign near the entrance says "Duke Burger - 0 Burgers Sold"; a play on the McDonalds gimmick of putting their burger numbers on their signs.
- In the SPCH building with the kennels and cell doors, one of the cells is titled as "Scrappy Due" and there is a cute little puppy in there, which you can kill. This is a reference to Scrappy Doo from the Scooby Doo cartoon series.
- The SPCH building itself (Society for the Preparation of Canine Hamburger) is a play on the SPCA (Society for the Prevention of Cruelty to Animals) from real life.
- When you operate the ordering machine, the voice "Go away, we're like, closed." is originated from Beavis & Butt Head.
Duke Burger also appears as a secret level in Duke Nukem 64, taking place after Gun Crazy (which, in itself, is a heavily-censored version of the Red Light District level). The enemies and weapons are also modified, due to this secret level taking place relatively early in the game, rather than the fourth episode; thus leaving you with less-advanced gear and less-intense baddies (i.e. no Protector Drones or Enforcers to deal with). The ending is also vastly different in the N64 version, as you are trapped before hitting the Auto-Destruct Button, and subsequently end up in Death Row.