[SteveNash3424213421J]

MGS3
Big Boss trained by The Boss.
The Boss betrays the US, joins USSR.
Big Boss sent in to kill The Boss and destroy the precursor to Metal Gear.
Big Boss meets EVA who turns out to be a spy working for the Chinese, she's "Big Mama" in MGS4.
Big Boss meets Ocelot, the Son of The Boss.
Big Boss turns out to be working with the US all along. She was sent in to steal the Philosophers Legacy, a list of bank accounts for the US to control the world. A nuke gets detonated so she has to pretend that she's betraying the US and has to die to cover it up all to protect the US. Ocelot ends up stealing the legacy and giving it to the US before EVA could give it to China.

MGSPO
Big Boss is kidnapped and imprisoned by the CIA. He is given up to a rogue faction of the US government named FOX sent in to kill their leader and destory Metal Gear.
Their leader Gene is setting up a nation for mercenaries and wants to use Metal Gear to destroy the Patriots (US branch of the Philosophers).
Big Boss kills GENE, stops the nukes, finds out that the US government was using him.

Some time betweeen MGSPO and MG1 Big Boss decides to turn "evil" There's supposed to be a MGSPO2 sometime.

MG1
A nation of soldiers called Outer Heaven is set up in Africa building up arms/Metal Gear planning to take over the world.
Gray Fox investigates, sends a transmission.
Solid Snake is sent in to investiage, saves Gray Fox.
Finds out Big Boss that was working for you is the main villian (this is the first game in the series to be released so you don't know at the time that he is "bad").
You destroy Metal Gear but Big Boss escapes.

MG2
Oil crisis around the world, Big Boss kidnaps a scientist that has developed a method of turning algae into fuel.
Solid Snake is send in.
Solid Snake gets the formula for creating algae to fuel but the scientist dies.
Gray Fox has switched sides and is in Metal Gear. You destroy Metal Gear and "kill" Gray fox.
Then you "kill" Big Boss.

MGS1
US special forces FOXHOUND led by Liquid Snake has gone rogue and has taken over a nuclear facility housing a new Metal Gear.
Solid Snake is brought out of retirement to destroy Metal Gear.
Solid Snake meets Meryl, your commanding officers daughter, she was a soldier guarding the place when FOXHOUND took over. She helps you throughout the game.
You also meet up with Otacon a scientist who helped designed Metal Gear but didn't know it was used as a weapon.
You meet Deep Throat which turns out to by Gray Fox in a cyborg exoskeleton that ends up helping you in the end.
And Naomi Hunter who is the doctor on your mission. Certain people around you have sudden heart attacks and you find out that Naomi injected you with Foxdie a virus that can target specific people.
You fight Revolver Ocelot but the Cyborg Ninja slices off his arm before you can kill him and he runs off.
You find out that Liquid is your twin brother. You were both clones of Big Boss. He got all the recessive genes.
Liquid is about to kill you but he dies from Foxdie. Naomi tells Snake he's a target and she can't say how long he has to live.
At the very end of the game Ocelot is talking on the phone to the President. Ocelot says that no one knows there is a third clone that's acting as president named Solidus.

MGS2 is pretty hard to understand so I'll split it up into two sections like the game does.

Tanker
Ocelot sold the Metal Gear plans around the world and now nuclear armed tanks are being built all around the world.
Solid Snake and Otacon set up Philanthropy to destroy the Metal Gears.
The Government has started work on Metal Gear Ray that's being built to take down all the other Metal Gears.
Solid Snake is sent on board the ship housing the Metal Gear Ray to take pictures of its existence and expose the government.
While on the tanker a group of terrorists board the ship and plan on stealing Ray for themselves.
Snake fights Olga one of the terrorist leaders daughters, Snake defeats her and afterwards a flying drone takes his picture onboard the ship. Olga also is pregnant with Sunny who appears in MGS4.
Snake takes the pictures of Ray.
Ocelot comes to steal Ray and it's shown that he has Liquid Snakes arm grafted onto his own where Cyborg Ninja cut it off. The Liquid can sometimes take possession of Ocelot and he's now known as Liquid Ocelot.
The tanker sinks, causing a massive oil spill and Solid Snake labeled a terrorist due to the pictures of him taken on board the ship.

Plant
2 years later an oil cleanup facility has been built in the place where the Tanker sank.
While visiting the Tanker, the current US President is kidnapped and held hostage by a terrorist group named Dead Cell.
Raiden meets up with Pliskin who is Solid Snake in disguise, they along with another cyborg ninja named Mr X team up and find the President.
The President tells you that the Patriots are in control of everything. The cleanup facility is just a cover for Arsenal Gear which houses an AI supercomputer called GW that is controlling the flow of information through the internet.
Raiden goes to meete Emma, Otacon's sister, who works on Arsenal gear to install a virus to disable it.
While going to upload the virus Emma is attacked and killed by Vamp and immortal, bisexual, vampire who appears in MGS2.
You upload the virus but it does not fully disable Arsenal Gear.
Mr X reveals herself as Olga and knocks Raiden out. She is working with the terrorist leader against the Patriots.
The terrorist leader is revealed to be Solidus the former President. He wants to set of and EMP in NYC to take down the Patriots and GW.
Liquid Ocelot then comes in. Olga reveals that she is a double agent working with the Patriots to complete their mission. Solidus kills her.
The entire mission turns out to be a test for how much the Patriots control.
It's a simulation for Raiden using similar events in MGS1 to make him the perfect soldier.
Liquid Snakes arm takes over Ocelots body completely and now wants to kill off the Patriots. He knows where they are know since he took over Ocelots body.
Raiden ends up killing Solidus.
At the end of the Otacon has found the names of all the high ranking Patriot members. Then tells Solid Snake that they've all been dead for over 100 years.