Remove the perk limit
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In the Mule Kick room on the left side there is a communication device lying on a night table. Pick it up and go to the control panel near the VTOL turret trap.  Insert the device and a UFO will come by and beam down a perk bottle.  Collect the bottle once it's landed and the perk limit will be removed.


Character quotes Easter Egg
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There are 4 picture frames with "interesting" pictures on them.  Shoot them while playing as the corresponding character and your character will make a funny remark about them.
Russman - Shoot the picture of manly Mona Lisa in the Jugg room
Stuhlinger - Shoot the picture of toothless dude in the spawn room
Misty - Shoot the picture of Dr. Sins in the Double Tap room
Marlton - Shoot the picture of Avatar Aang in the Mule Kick room


Radio locations
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Radio 1 - Located in the spawn room on top of one of the work stations.  Features Dr. McLoughlin observing element 115 under a microscope before the Shadowman was released.

Radio 2 - Located just to the left of one of the rocket trap activation switches laying on top of some boxes.  Features Dr. McLoughlin running for safety as the Shadowman uses his undead army to swarm the base.

Radio 3 - Located on the bed near the B23R wallbuy.  Features Dr. McLoughlin stitching his wounds days after the initial attack on the base.

Radio 4 - Located inside the secret Easter Egg vault room next to the skeleton.  Features Dr. McLoughlin's final message before dying of dehydration.

Radio 5 - Located floating near the dead body in the Pack a Punch room.  Features Joey dying for the third time in 3 maps after being abandoned inside a satellite.


EE song (Lost by Kevin Sherwood and Craig Houston)
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Teddy Bear location 1 - On the 2nd floor of the spawn building on a shelf
Teddy Bear location 2 - In the Double Tap room cradled inside of the power generator
Teddy Bear location 3 - In the Mule Kick room on top of one of the beds

Secret EE song (Rocketman by Elton John)
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On round 28 or after shoot the very tip of the rocket and the song will play

How to get Galvaknuckles
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I don't really consider this to be a side easter egg because I think it's obvious but I'm putting this here anyway in case you don't understand.
Step 1 - It's on a piece of sheet metal hanging from the crane.  Just jump off the top platform and buy it on the way down.