One of the girlie magazines you can pick up features Alexandra Roivas from Eternal Darkness. Just open the magazine and zoom in to see her in a bikini.
Alternate Ending
Instead of hurrying back to fight Sniper Wolf and save Meryl, or holding out while being tortured by Ocelot, do whatever you can to allow Meryl to die during the course of the game. Then, instead of riding off to a happy ending, Snake will simply ride off on his snowmobile all by himself to fight another day.
Alternate Ending Theme
Successfully complete the game three times on any difficulty setting for an alternate ending theme.
Anubis Poster
There is yet another egg in the Otacon's office. On the wall is a poster of Zone of the Enders: Anubis, which Otacon mentions during the cut scene. Fans of the game will recognize the poster as the game's box art.
Bandana, Camera and Extreme Difficulty Setting
Successfully complete the game on any difficulty setting to unlock the Bandana, Camera, and extreme difficulty setting. When you equip the bandana you can use an unlimited amount of ammo and will not have to reload your gun. After you receive the camera there will be an "Album" option on the main menu, use this option to view pictures that have been taken.
Escape Medical Room Prison Variation
After the torture room scene, Otacon will come to Snake give you all the items you need to escape the holding cell. Alternatively, if you wait even longer the Ninja will come and open the door for you.
Eternal Darkness Poster
In the Armory, B2 of the Tank Hangar, there are six separate rooms. If you go inside the top far right room, there is a locker with an Eternal Darkness game poster inside.
Eternal Darkness Reference
One of the magazines found in the game has a picture of Alexandra Roivas wearing a bikini. Pick it up, open it, then zoom in on the contents to find her.
Gain Extra Health
During the Ninja boss fight, shoot the Mario figure on the desk to gain extra health.
GameCube and Wave Bird
In Otacon's office, take a look at the desk to find a GameCube and Wave Bird. In addition, look at the monitor nearby to see the GameCube boot-up screen.
Get Liquid's Dog Tag
While in the hand-to-hand fight with Liquid, get him near the edge. Once there, start your punch combo, then finally kick him off. He will grab on to the edge, and as he does, his nametag is up for grabs.
Get Peed On and Make Friends with Wolves
After fighting Psycho Mantis, follow Meryl through the wolf den. At the end of the den Meryl will be waiting with two wolves. Hit Meryl once and then quickly hide inside of a box. Meryl will instruct the pup to pee on Snake. You can now walk through the wolf den, while having the box equipped, without being attacked by the wolves.
Make Mei Ling Mad
Using your very cool and high tech codec call Mei Ling. When giving the option of saving or not select not saving. Do this a few times and eventually she'll give you a brief talking to and she'll stick her tongue out. Not very professional Mei Ling.
Meryl Demo
Successfully complete the game on any difficulty setting without submitting to Ocelot when being tortured to save Meryl.
Meryl in Her Panties
When in the Holding Cells area, crawling through the vents to find the DARPA Chief, you'll first see Meryl doing exercises in her cell. Before going forward to meet the DARPA Chief, exit the vent the same way you came in and re-enter to see Meryl doing exercises in her undewear. You can leave the vent and come back once again to see her performing other exercises.
Meryl in Her Panties (another one)
We all know Snake is a ladies man (and a pervert,) so I believe this cheat suits him. After the battle with The Ninja you are sent on a mission to find Meryl who is wearing and enemy uniform on the floor B1. Once you discover her she will the make a run for the girls bathroom to the right of the elevator. Be in hot pursuit and make it to the bathroom at least a few seconds behind her and through out that whole cut seen she will be in her underwear. You go Snake!
Meryl’s Taunt
After you go through the wolf caves and end up in the minefield (right before Meryl gets shot by Sniper Wolf). After Meryl crosses, run into a mine. Keep doing this. Meryl will then whistles and slap her rear. Repeat this to see her do it again.
Meryl's Costume
Successfully complete the game twice on any difficulty setting without submitting to Ocelot when being tortured to save Meryl.
Otacon Demo
Successfully complete the game on any difficulty setting with submitting to Ocelot when being tortured to not save Meryl.
Otacon's Costume
Successfully complete the game twice on any difficulty setting with submitting to Ocelot when being tortured to not save Meryl.
Outer Heaven Nametag
After the scene where the Ninja kills all the soldiers outside the Lab, Look at the soldier closest to the door. You have to look down using your scope, but his nametag says "Outer Heaven". You'll get a better camera angle if you look at it upsidedown.
Perform Exorcisms
After you find the camera, in a level 6 security door behind a destructable wall in armory south, take pictures of random stuff. When viewing the pictures, you will see other pictures of some freaky stuff laid over top of yours, and there will be a new option that says "exorcise". All this does is makes the ghost go away, so do not do this if you like the way it looks.
Verified Ghost Photos:
1. The Dead DARPA chief (in the medical room holding cell, not Decoy Octopus)
2.The bust with the bandages on it's face on the left side of the Command Room (where you fight Psycho Mantis)
3. The mirror on the right side of the command room (where you fight Psycho Mantis)
Psycho Mantis Comments
Having saves from various games on your card such as Eternal Darkness, Legend of Zelda: The Wind Waker, Super Mario Sunshine, or Super Smash Bros. Melee will allow you to hear specific comments made by Psycho Mantis during the boss fight.
See Yoshi and Mario
After your battle with Ninja, take a time to look around Otacon's office. You'll see a Yoshi and Mario statue on a filing cabinet. Shoot the Yoshi and he will make his classic noise. Shoot Mario and a 1Up will appear above his head. In addition, you will get a health bonus with each 1Up.
Stealth Camouflage and Tuxedo Costume
Successfully complete the game twice on any difficulty setting to unlock the stealth camouflage and tuxedo costume. When you equip the stealth camouflage enemies (except bosses) and cameras will not detect you.
Upset Meryl
Right after you meet Meryl in the Restroom of the Nuke Building, Go into first person mode and stare at her breats. She will spit out comments like "Why are you staring at my...?" or "Don't look at me like that!"
Zone Of The Enders Reference
Look at one of the posters in Otacon's office to see the graphic from the front of the Zone of the Enders: The 2nd Runner box.