Metal Gear Solid 2: Sons of Liberty/Arsenal Gear and New York: Eliminate Solidus

Arsenal Gear, Stomach: Torture Chamber 

When Raiden wakes up he will be choked by Solidus and you will have to tap Triangle repeatedly to hold your breath. In Very Easy mode, you don't have to do this at all, as the O2 gauge will not even reach the bottom before it stops, but in contrast, European Extreme is very hard. You may want to use a speed controller.

When that is done, after a few codec conversations and other various cutscenes, Raiden will find himself naked in a room that is identical to the torture chamber in MGS1.

He will be unable to enter hanging mode, choke enemies, or throw enemies because he is covering his nudity (presumably he is insecure and doesn't want the anonymous soldiers to see his jiblets). He can however still perform the punch-punch-kick combo.

Anyway, head east and open the locker; there is some cold medicine which will help. Head through the door and log into the node. Then leave through the door to the east.

Arsenal Gear, Jejenum: RAY Storage

Back against the container and go all the way to the right. Wait until the soldier here turns around, then head east and round the second container here, and then up the stairs. Listen to the codec conversation then back up against the wall up at the top of the stairs. Wait until the guard here turns around then head west along the walkway.

Grab the box here and go north until you reach a camera. Head by it then sneak to the far north of this side of the walkway. When the guard on the other side turns around, head east towards him then north. Hide behind the box here and when the coast is clear, head east into the tunnel.

Arsenal Gear, Ascending Colon: Tunnel

Head south and grab the ration, then walk up and down, answering each codec call. Eentually you'll get one from Rose, and Snake will appear with your gear. He'll also give you a sword. If you want Snake's dog tag, beat him up and shake his unconcious body; but be careful, when he wakes up he'll be pretty pissed. When you've practiced enough, head north.

Arsenal Gear, Ileum: Munitions Storage Take out all the guards here, Snake will help, and keep moving North. When you're done, head North again. Grab the ration.

Arsenal Gear, Sigmoid Colon: VR Simulator Another similar sequence will occur, but this time, a mock-game over screen will occasionally appear. Ignore it. You'll notice it says "Fission Mailed". Tee hee hee!

Arsenal Gear, Rectum: RAY Testing

Solidus will be talking to you. Run around and pick up supplies.

BOSS: Mass Produced RAYs

See Bosses for more info.

Arsenal Gear, Exterior

When this is done, you'll experience a similar choking sequence as before, but much harder. A tip is to look all the way to the left or right; this makes the bar deplete slower.

Federal Hall

Finally, you will, after around an hour worth of cutscenes, fight Solidus on the roof of a building in New York.

BOSS: Solidus Snake

See Bosses for more info.

Finally, after another movie's worth of cutscenes, the credits roll! Then more cutscenes! Then you have completed the game! Woo!