So there's this Illuminati group called the Philosophers made up of America, China, and Russia back in the late 19th century and early 20th century who broke apart due to personal differences. They had a whole fuckton of billions of dollars called the Philosopher's Legacy. This chick called The Boss, who is the greatest soldier of the 20th century, got sent in by America to infiltrate Russia as a pretend double-agent to get their portion of the Legacy, but after a misunderstanding a nuke was fired, she got framed for it, and Russia was ready to go to war.

So her greatest student, Snake, got sent in and after kicking the shit out of a bunch of old dudes, wound up killing her and becoming Big Boss, the new greatest soldier of the 20th century. Meanwhile The Boss' son, Ocelot, got his ass kicked by Snake/Big Boss and saw him as his new mentor/gay lover. He'll become important later. Then Big Boss found out The Boss wasn't a traitor at all and loved her country, which made him bitter and sow the seed of unrest in his soul.

After some bullshit happened he broke away from America and made a military group with a French name I can't remember, his own private army. Meanwhile his old friends formed a new Illuminati called the Patriots and invited him to join since he was the most skilled and famous soldier in the world. Then his army got blown up so he made another along with a full nation of soldiers called Outer Heaven, which happens in MGS5. Also he got put into a coma for nine years during which the Patriots cloned him three times, forming Solid Snake, Liquid Snake, and Solidus Snake. He got pissed at being a clonedaddy so he left the Patriots, took his nation and went rogue, threatening the world with nuclear armageddon using Metal Gear, a giant robot that can fire nukes anywhere on the planet and bypasses most arms treaties.

Solid Snake got sent in to kill Big Boss but failed. Then he got sent in to kill him again and succeeded. So now Solid Snake is the new greatest soldier in the world.

Liquid got jealous that Solid got all the glory so he got himself a Metal Gear, a crew of badasses, and an army of soldiers with Big Boss' DNA implanted. Then Solid blew it all up and killed him, but Ocelot, who got his arm cut off earlier, stitched Liquid's arm onto the stump and got possessed by Liquid's ghost. Then it turns out Ocelot was working for Solidus all along, who is the president of the United States.

Solid gets framed for a terrorist attack and goes into hiding with his nerd friend Otacon, who built the Metal Gear Liquid had.

Two years later, some white-haired bitch named Raiden gets sent into an oil plant to fight terrorists. Except it's all just a simulation to see if he could become like Solid Snake if he goes through the same stuff Snake did in MGS1, but the real Solid Snake helps him see through the bullshit. Raiden kills Solidus while Solid Snake goes after Ocelot, who stole another Metal Gear.

Then Ocelot, who is still possessed by Liquid except it wasn't Liquid's ghost but hypnotherapy making him think he's Liquid, takes over the world using nanomachines. Also Raiden is a kickass cyborg now. Snake (who is old as fuck because of accelerated clone aging) blows everything up, then duels him atop Outer Haven, Ocelot's Outer Heaven-ripoff shit. Snake kills him and then everyone goes home happy, except for Snake because he's dying of a disease he got in MGS1.

I skipped over a hell of a lot but that's the gist of it.