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Here I have compiled all the known facts about Snake Eater and what i have concluded from them.

Press
 
E3 2003
Trailer
Slogan "Back To The Origins"
Snake Missing Eye in Flames Scene
Use of Russia, Peace and Bomb Icons
You need to eat creatures
Sneaking is Even more essential!
Creatures: Dogs
Locations: Jungle, River & Docks
 
Press Release
Hidden big boss message
Use of 1961 - 1964 history
Old map of Russia, specifically Zanzibar Land!
Picture Snake covered in Russia & USA Flag
List of Words include camouflage options and specifically Viper and Cobra!
The new Metal Gear! hidden in craft sheets (Confemed in E3 2004)
 
TGS 2003 / Playstation Experience 2003
Trailer
Silouette of Metal Gear on front legs (Launch Posistion)
Slogan "Honeyed Espionage"
First Sights of Close Quarters Combat (CQC)
First Play of Snake Eater Theme
Use of Gavial head wear
New Creatures: Bats & Gavial
New Locations: Cave and Underground River
 
Camouflage Demonstration Video
First viewing of camouflage stealth bar
The Jungle is shown to be more corridorish than was first hoped
Camoflague section is essential for fast and silent movement
 
E3 2004
Trailer
Confermation of the year being 1964
First ever HALO jump
Complete scene of Snakes landing
We Meet Solokov (Traitor) & Eva (Livewire)
Solokov is the creator of the Metal Gear (Hornet)
First true pictures of Metal Gear in launch position
Slogan "MGS Relives Yesterday To Survive Tommorow"
Ocelot Unit Defeated by Snake
(Revolver) Ocelot is the Major of the group
Thunderbolt is the destined runner of the Metal Gear
Thunderbolt is the one who gives Snake his eye patch after a whopping!
New Soldiers: Heavy Infantry & Flame guyes
New Creatures: Vultures
New Locations: Mountains, Bridge, "Bunker" and Red Brick Hanger
New Vehicles: Hind-D, Hover Craft & Turret Station
Words of loyalty's, Truth and Betrayal
Snake with infamous Eye Patch!
Snake surgests Ocelot uses Revolvers according to his style
A Ivan looks like Raiden (Even has the Nut test!)
Ocelot Juggling 3 Revolvers :)
 
Press Kit
TPN - Russian for 3
Meme x Gene x Scene = MGS3
Meme = Memorys - Remembering 1960's ect... MGS3
Gene = Genetics - Creation of Les Enfant Terrible and Sons of Big Boss MGS
Scene = Scenario - The Patriots S3 Plan / Big Shell MGS2
First picture of FOX unit logo
LP containing CD of "Snake Eater -Abstract Camouflage-" (Remix)
 
E3 Demo
14 Minute Intro Sequence
We have an exact date! 24/08/1964
Big Boss is actually codenamed "Naked Snake" (Jack/John Doe)
Theirs no codec but a radio system and slide info on the person your talking to.
Your Stamina will drop quickly so eating grub is essential.
As you eat a food bar will show your opinion of it and how many times you've eaten it.
The Demo runs from enterance to introduction of Ocelot
 
GGC 2004
Trailer
Confermed as 60's & The Cold War
The Boss is confermed as the Traitor
The game is confermed to have 2 chapters
The Metal Gear is called Shagohod
Snake & EVA is pursued by Metal Gear
Also Ocelot and a few more men
The first mention of "The Patriots"
 
TGS 2004
Trailer
Shows who The Cobras are
The Boss confermed as leader
Shagohod can crawl!
Futher battles with The Boss shown
Events of Snake losing his eye!
Event of Snake in his cell, with Johnny as the guard
Ape Escape mini game!
Surgestion of Ivan being a member of the Patriots!
 
Kit
Shows Exclusive Screen Shots
Details on the games attributes
Cobras Revealed
Artwork of all the currently revealed characters!
Advertisement of MGS3 the Countdown and Premium Package
 

 
Other:

Big Boss is Snake!
A Few good reasons for this
1. The E3 2003 press pack hides "big boss" letters in the insert
2. The E3 2003 trailer shows an eye missing
3. Being based in 1960's Solid Snake wasn't born until the 1970's!
4. The E3 2004 trailer features the infamous Big Boss with Patch!
5. The TGS 2004 trailer shows Snake loosing his left eye!
6. The Boss talks of only one surviving to become Boss!
Thanks to some promotional dog tags we now know the REAL NAME of Big Boss: "Jack T Millies"
CONFERMED
Also a member of EGM has confermed it after playing the game!
 
Metal Gear What!
The New Metal Gear Will be codenamed the Shagohod, but is actually not a Metal Gear as it isn't bipedaled.
CONFERMED
 
Mystery Lyrics
In the ECTS trailer, their is a section where the female singer gives a James Bond esq ballard, but part of the lyrics says "Im in a dream Snake Eater" which turns out to be said twice and also while Kojima's name is said, coincidence i think not.
I sense that Solid Snake will be in the new game
This Theory is now concluded to be false and is more to do with us reliving the Cold War
 
Surprises Facts
Thanks to Konami and Showbiz letting slip some info here are NEW FACTS
 
Cast List
CIA Cheif (Awards Snake "Big Boss" codename)
Commander (The person in the Combat Talon with Snake)
Director Glanin (Creator of Metal Gear Rex)
Director Sokolov (Creator of Shagohod)
Enemy Soldier (This can be multiple people)
EVA (A mole in the GRU Slide4))
Guard Johnny (Johnny's dad)
Hanger Intercom (Shagohod's hanger)
Ivan Raidenovich Raskov (GRU Lieutenant and secret helper)
Khrushchev (The Russian President of the 60's)
Major Tom/ Major Zero (Your contact)
Mig Pilot (He chases your 2nd entrance aircraft)
Mr Sigint (A high tech weapons and history specialist)
Ocelot (A young Revolver Ocelot)
Para-Medic (A femail medical specialist)
Parrot (The End's)
Pentagon Official (One of the patriots!)
President Johnson (US President of 60's)
Snake (Big Boss (Slide3))
The Boss (Snakes mentor & Ocelots mum!)
The End (First ever Sniper)
The Fear (High mobility foe Slide1&2)
The Fury (Burned Man who loves flames!)
The Pain (God of Bees)
The Sorrow (Ocelots dead dad)
Thunderbolt (Colonel Volgen) (The Leader)
US Department Of Defence Official (One of the Patriots!)
 
Voice Actors
Naked Snake / Jack / Big Boss: David Hayter
Major Tom / Zero: Jim Piddock
Ocelot / Adam Shalaska: Joshua Keaton
EVA / Tatyana: Suzette Mińet
The Boss / Joy: Lori Alan
The End: J. Grant Albrecht
The Fury: Michael Bell
The Fear: Richard Doyle
The Pain: Gregg Berger
The Sorrow: David A. Thomas Jr
Director Sokolov: Brian Cummings
Director Granin: Jim Ward
Colonel Volgin: Neil Ross
Ivan Raidenovich Raikov: Charlie Schlatter
President Johnson: Richard McGonagle
Chairman Khruschev: David Thomas
Commander: Jesse Corti
US Department Of Defence Official: Fred Tatasciore
CIA Director: Paul Collins
Johnny Sasaki Sr.: Michael Gough
Soldier: Scott Menville
Soldier: Robin Atkin Downes
Soldier: Charlie Schlatter
Soldier: Mathew Kaminsky
Soldier: Michael Gough
Soldier: Philip Tanzini
Soldier: Chris Cox

Solid Snake: David Hayter (Mini Game)
Roy Campbell: Paul Eiding (Mini Game)
 
 
Storyboard Slides!: 1 2 3 4 5 6
Character Stills from the Official MGS3 Site
 
Mech
 
Your 2nd Entance Plane!
A rather nice surprise that i've found out, according to the Mig pilot the craft was flying at Mach 3, a Combat Talon can only do 300 Mph, while Mach 3 is a massive 2151Mph! the only craft in the world able to do this is the BLACKBIRD and it stated service in 1964!
The one in the Trailer is the Prototype which wasn't painted
CONFERMED
 
The Pod
The pod Snake lands in the 2nd entrance is called the D-21 Drone, produced along side the Blackbird it is capable of Mach 3 also. Normally this is just a recon drone that then crashes after doing its mission, although not many where actually used, the one here was specially modded for a passenger and has specially fitted reverse thrusters. (This is later destroyed by The Boss)
CONFERMED
 
Meaning of Vituous
Virtuous: of moral excellence; "a genuinely good person"; "a just cause"; "an upright and respectable man"; "the life of the nation is secure only while the nation is honest, truthful, and virtuous"- Frederick Douglass. This man was a former black slave and consultant to Lincoln, his papers ended in 1964!
CONFERMED
 
Who are the Cobras?
They are a Special Forces group run by The Boss, which is secret much like F.O.X the members all have incredible gifts, which they were either born with or gained during their lives.
CONFERMED
 
Who are F.O.X?
A Secret stealth agency in the US government called Fox Operations X who was supplied with every possible piece of gear available then and in development.
The F.O.X was created for one reason… to prevent a nuclear war and to protect the motherland from threats.
CONFERMED
 
Hunting your dinner…
New information has come to light, unlike what was seen in the E3 2003 trailer when you kill something it turns into the familiar rations, but unlike the other Metal Gear games this food soon goes off and is poisonous to eat causing Snake to suffer nausea and to be sick!.
If the meal is tranquillised the food is caged to be either let loose on unsuspecting guards like dangerous creatures and keeping food much longer to eat.
CONFERMED
 
Control system
Its come to light that the stalking will be allocated to the D pad while walking and running will stay on the analogue stick. The CQC will also be simply activated by one press of the triangle (Action Button) once you get close enough.
CONFERMED
 
Special Power Camos
Their are 4 currently confermed
Water Camo: Accelerates Swimming
Fire Camo: Prevents Burning
Snow Camo: Helps in colder weather
The Boss Camo: Accelerates Movement
CONFERMED - These come from non letheal kills of the Boss'es and from back tracking
they also cover face pains which included Attraction, Infinate ammo, air, grip and duck mask!
 
EXTRA MISSION!
Recently revealed was a mini game called Snake vs Monkeys, this is part of something called Extra Missions!
Originally from ZOE2, this is only accesible after completing the game, other missions included:
Time Attack, CQC Challenge, Boss Battle and Special Event
 
BUT ALSO THEIR WILL BE SNAKE TALES!!!!???
 
Consisting of 4-5 chapters the missions involve the following:
Naomi: The Mission to rescue her from Prison
Olga's Clild: The Mission to rescue the child and find out the father
GREY FOX!: Little is known on this one...
Liquid: A Mission on Vendettas and one final Ray battle! rumoured to be in New York!
FALSE! - this may still appear in the European edition, but is unlikely
 

 
The Facts So Far...
Radar Optional (Sonar, AP Sensor & Motion Detector Confermed)
Silenced Weapons will degrade with use
Big Boss, Eva, Ocelot, The Boss, Thunderbolt, Sokolov and the Cobras Confermed
Presidents of Time Confermed
1st chapter based exactly on 24th October 1964
Shagohod confermed as E3 2003 Paper Craft
Codec is now retro with sheets on contact
Eatings essential & a board displays Snakes tastes
Camo has been simplified for easy use
Johnnys Back HURRAY :)

Weapons:
Survival Knife, MK22, M1911A1, Colt Single Action Army, XM16E1, AK-47, M63, M37, SDV, RPG-7, Grenade, WP Grenade, Stun Grenade, Chaff Grenade, TNT, Claymore & Directional Mic
Items:
Binoculars, Thermal Goggles, Night Vision Goggles, AP Sensor, Motion Detector, Active Sonar, Mine Detector, Cigar, Pentazamin and Gavial Cap
Vehicles:
Jeep, Bike, Hind-D, Hover Platforms!, Armored RV & Shagohod
Guard Types:
Light, Heavy, Flame & Pilots
Creatures:
Gavial, Dog, Vulture, leeches, Rat, Snake, Frogs, Bees & Bats
Locations:
Jungle, Mountain, River, Dock, Hanger, Wood Hut, Bridge, Bunker, Cave Complex, Hanger, Airfield and GRU Headquarters
 


My Conclusions from facts so far...
The game will be based ONLY in the 1964 and will take place over 2 periods one being 24/8/1964, with the Snake Eater chapter being prior to 16/10/1964.
The Patriots will have a very strong affect on this game.
VERY TRUE - 2nd Chapter 1/10/1964
 
The mission:
 
PLEASE NOTE THIS IS MY INTERPRETATION FROM COMBINING ALL AVAILABLE FACTS!
 
Note text in this colour was confermed correct
Earlier Later
 
The game consists of 2 chapters
1. Halo / Virtuous Rescue Chapter (Mayor Tom)
2. Blackbird / Snake Eater Chapter (Mayor Zero)

Halo / Virtuous Chapter.
Mission to retrieve Sokolov & escape in the Fulton Surface to Air

Snake flies in by MC 130 Combat Talon and does a Halo Jump into Tselinoyarsk, landing lossing his backpack you go back to the tree to retrieve your gear, now able to proceed , Snake sneaks or shoots (players decision) to get to Sokolov in the Abandoned factory, after a discussion with Sokolov about Volgens men, Snake leads Sokolov out only to be confronted by the GRU, then Ocelot shows up and takes out the GRU followed by Snake taking out his fellow Ocelots(#1).
Regrouping with Sokolov who is hiding they make their way back to the Escape point, on the way Sokolov points out his creation resting on a nearby mountain.
Crossing the bridge Snake sees a figure in the mist and stops, it was The Boss! Asking why she had defected she explains The End asked her to. In the battle that followed Snake falls from the Bridge gripping her bandana.
Recaptured Sokolov is taken by Thunderbolt as they board a Hind.
Snake watches on as they fly off with in one of the five Hinds carrying the Metal Gear.
Thunderbolt uses one of the "Gifts" to nuke the OBK 754 nuclear research facilty.
Snake manages to escape by using the Fulton and is picked up by the Combat Talon.

Talk between President Johnson & Khrushchev

Blackbird / Snake Eater ChapterSnakes mission is to find and kill The Boss to prove America wasn't behind the attack and to destroy Shagohod.
Note: Volgen is allied by Brezhnev Military faction (Future Russian President) & The Boss is leading THE COBRAS!
Snake returns to Glasnigrad in Russiaon a Blackbird onboard a pod thats on the top, being persued by 2 Russian MIG's who are now on high alert to intruders going into Russian airspace.
Snake lands but this time he has no gear.
looking for his pod he finds The Boss waiting nearby... Now in new gear, she destroys the Pod and takes off by Horse
but not before telling Snake were to find Sokolov and stomping on Snakes hand!. making his way through the forest Snake trapes through a river and is confronted by a Silluette which turns out to be The Sorrow, after defeaing the undead! they chat (what ever that is) Locating Sokolov, they make their way towards the hanger area, crossing a bridge Sokolov is mysteriously lifted by some bees and is throw to his death, now chased a mass of bees! Snake escapes by diving off a waterfall.
Getting out he is confronted by The Pain! (
Battle)

Defeated Snake carries on discovering this failure The Boss orders The Fear after him finding snake in deep forest he shoots a dart into his leg, in agony he carefully pulls out the dart, looking up to see who had shot him, The Fear introduces himself (Battle)
Able to continue....
Snake finally reaches the mountainous area and just as he's about to climb the path The End shows up (Battle)

Passing the mountainous area was dificult since snake had to battle his way past hover craft, Hinds! and flame guys!
At the top Ocelot challenges him to a duel (Battle)

Passing the mountain area, Snake comes accross an abandand structure, where he is faced by a biker! after discovering it was Eva they talk on what they have both found out so far.
Using Eva's transport they travel to the outskirts of the Hanger area, but not before a bike chase with Ocelot and the GRU! leaving Snake to sneak in he passes in through a secret door in the Docks area and then up some ladders.

Reaching the hatch he regroups with Eva and they both do some reconisance.
Sneaking inside Snake meets up with Glanin to try and find out what the Shagohods weakness was.

leaving the room snake continues to the main area, but not before meeting The Fury! (Battle)

Carrying on Snake reaches the main hanger and begins to plant the charges,
while on his escape Thunderbolt introduces himself and denounceshe has the ultimate keys The Shagohod and The Cobras!

Realising he has no time left Snake runs off in the nick of time to escape the collapsing building!
Meeting outside with Eva Snake finds out the Shagohod is not destroyed as it crawls out of the burning building having to rush off Snake and Eva try their best to avoid the chasing mech, using his rocket launcher snake targets the areas Glanin had surgested. After a while the Shagohod is defeated but in the following Explosion Eva and Snake are knocked unconcious...
Waking up Snake finds himself alone in a room with The Boss and Volgen, trying to reach his weapons The Boss stops him using many CQC techniques, injured he is hung by his hands.
With Volgen watching the boss removes one of Snakes eyes
but instead off cutting the other eye she knock him out.
Awakening Snake finds himself in a cell in major pain! talking to the guard (Johhny) Snake has a short chat about families, friends and the Cold War.
At one point Ivan comes in and as Johnny salutes he knocks him unconsious!
Allowed to escape Snake first collects his gear and makes his way out, but not before being once again being confronted by Ocelot (Battle)
Carrying on Snake meets up with Volgen, enraged to see him out he tells of what has happened to Eva for betraying her! As they fight Volgens suit gives him the upper hand as he beats the stuffing out of Snake! As Ivan come in the room Volgen orders his subordinate to take him back to the cells. as he says this Ivan pulls a gun and kills Volgen at point blank range.
Allowing Snake to escape snake makes his was to the agreed point on interception.
At this place Snake meets The Boss for one final battle to decide who should be Boss (In white flower fields) (Battle)
Being victoriuos Snake boards the recovery craft.
Just as the door closes Ocelot jumps in and starts a hand to hand brawl!

(May just join forces here or be thrown out!)

Big Boss award ceremony

The End....