Were do you go on Metal Gear Solid 2 when you are in the new metal gear

"in" the new metal gear? do you mean when you are raiden and naked?
If so you'll get out there should be two doors two a big room try to find your way to the end of the right side you'll see a door go in it then run around answering your codec until rose calls then solid snake will come to the rescue with your stuff with a little present from olga.