IFC you want to collect dog tags, see this excellent guide
After the intro movie, head around the left side and collect the bandage from under the stairs. Now look out for the guard round the corner and deal with him however you like. Collect the RATION from the far corner, then go through the door at the bottom of the stairs.
DECK A, CREW'S QUARTERS
Follow the passage right then go into the locker room that you find. Open the bottom left locker on the left side of the room to find a RATION then search the bottom right locker on the other side of the room for some M9 AMMO. Leave the room and head right, take care of the guard and if you like, hide him in one of the lockers. Head along the passage and through the door at the end.
DECK A, CREW'S LOUNGE
After the short cut-scene, shoot the two guards patrolling the lounge. Go into the lounge and pick up the M9 AMMO from behind the bar and the RATION from in front of the plasma screen TV. Go up the central staircase and through the door on the right.
DECK B, CREW'S QUARTERS
Go up the passage and turn right to pick up the M9 AMMO from under the stairs. Go back and shoot the patrolling guard, then follow the passage and go up the other stairs.
DECK C, CREW'S QUARTERS
Look out for the camera in the next corridor and keep your back to the wall to avoid it. Open the locker to find some CHAFF GRENADES, go in the ventilation duct near the blocked stairway to get a RATION and then go up the stairs in the middle.
DECK D, CREW'S QUARTERS
There are quite a few guards patrolling this area and not many places to hide, so take care. If you think that you're going to get spotted, shoot! Head left into the dining area and pick up the RATION in the kitchen and some M9 AMMO under one of the tables. Now go back out the same door and head the other way. Go up and into the storeroom. Pick up the M9 AMMO and BOX 1. A guard may enter while you're in here so use the box to hide, or crawl under the central shelves, Also you can break the food on the shelves by melee. He soon falls asleep so use the opportunity to shoot him and leave the room. Answer the Codec message you get from Otacon, and he will tell you about the Semtex bomb in front of you. Shoot the guard on the other side, but don't walk through the Semtex! If you do, the game is over.Shoot the fire extinguisher to reveal the lasers, and crawl beneath them. Search the body for items and head up the steps.
DECK E, THE BRIDGE
After the cut-scene, head left and pick up the RATION then go through the door to meet Olga for your first Boss fight.
BOSS: OLGA GURLUKOVICH
Olga isn't too hard to beat, but she does like to hide and she has a couple of tricks up her sleeve. Early on in the fight, you'll want to shoot the spotlight and the small ropes attaching the tarp to the crates to dispose of it. If you don't Olga will use the light to blind you and the tarp to hide behind. The trick to beating Olga easily is to make her think you're somewhere you're not. Hide behind a crate and pop your head up so that she can see you, then as she's firing away at that spot, roll or crawl to a different spot to get an easy target to shoot at. Repeat this until the fight ends. Olga sometimes throws grenades if you don't do anything for a while, so watch out for that.
You now have a USP but no bullets, so you can't use it yet. Crap. Pick Olga up then drop her to get her Dog Tag then pick up and drop her a few more times to get some more items. Pick up the RATION behind the crate on the right then head right and up the steps. Climb the ladder right to the top of the mast to find the THERMAL GOGGLES, then climb back down. Go down the stairs, head right and take out the guard that comes through the door. Carry on over to the right to find the WET BOX (don't use this inside!). Now return to the Bridge via the door.
DECK E, THE BRIDGE
Pick up the USP bullets in here, then go down the stairs, get some USP Bullets from DECK D, CREW'S QUARTERS (under the table) and head all the way back to DECK A, CREW'S LOUNGE.
DECK A, CREW'S LOUNGE
Go down the stairs to the right of the lounge area, grab the STUN GRENADES at the bottom and head through the door.
Walk up the corridor to meet Vulcan Raven from Metal Gear Solid (sort of). Head through the door into the main Engine Room. You'll find a guard lurking right by the door, but you can slip past him easily. An efficient way to do this is to hit him over the railing and he might hit the guard on the bottom level, but take care of him quickly before he wakes up, or he will call an alert. At the top of the steps, aim down and take care of the guard below. Once at the bottom of the first set of steps, go right and approach the railings. Swing over and drop down onto the level below. Take out the guard and continue through the Engine Room, and go up the large set of stairs in the middle of the room. Go around the walkway and around to the left side of the room. Go up the steps and take out the patrolling guard at the top, then head through the door. Go up and watch the cut-scene, then take out the guard, but not until he has put his radio away. Go into the area with lockers, and climb on to the crate with the USP AMMO on it. Equip the THERMAL GOGGLES switch to first person view. Stand on tiptoe (L2 and R2) and use the USP to destroy the control box at the top right, with the green light on it. Carefully walk through the first part of the trap that is now vacant of traps, and shoot the last two control boxes which on the floor on the left hand side. Once through, open the door and head through.
DECK 2, PORT
Run down the passage and wait it the third bay on the right until the guard comes along and stops. Quickly run behind him and continue. At the corner, wait for the guard that is listening to music to appear, and take care of him or just slip past him. Run past the last guard when he nods off to sleep and go through the door.
DECK 2, STARBOARD
Run down the passage and watch the cut-scene and prepare to battle. Equip the RATIONS for the battle. Use your USP and blast away at the guards. If you are running low on health and RATIONS, go back towards the screen to find some supplies. Once the first lot of guards are dead, another three will storm in and charge at you. Just kill them as they come with your weapons and watch the cut-scene.
HOLD NO. 1
You should see a timer on the right, so try to move quickly. Climb down the ladders and go to the left towards the projector. In front of the projector, crawl beneath the beam of light and continue left. When you see the hatch in the corner, open it and go down. Simply crawl through the vents and try not to make any loud noises. At the end, come up out of the vents and through the nearby door.
Another way, before going down the ladders, get full LIFE and jump over the railing and climb out. What looks like nothing actually is a rope. Then climb across, and go across the other side and go through the door to Hold No. 2. For the upper way you must have GRIP LVL3. Do NOT kill or alert any of the Marines or it's Game Over.
HOLD NO. 2
This hold is pretty much the same as Hold 1. Again, go down the ladders, crawl around the projector, and go down the hatch. Crawl through, and once you reach the small break in the shaft, a guard's magazine falls through the grate. The guard will look down, but as long as you don't go through the patches of light, he won't see you. Follow the shaft all the way and directly into the next section. Or, you could just use the doors.
If you are on the upper level, as described before, do the same thing and go to the upper level of Hold No. 3.
HOLD NO. 3
After the short cut-scene, you will see that you are beneath Metal Gear RAY. Big isn't it? Anyway, head right and through the vent. Climb up the ladder and then slide down the pole. Head towards the screen, and carefully slip past the guard. Stay right and head towards the door, but don't go through! Instead, stand in front of the door. You need to take four photos of Metal Gear RAY - a front shot, a front right shot, a front left shot and a photo of the 'Marines' emblem on Meta Gear RAY's leg. Equip your camera and take a photo of Metal Gear RAY from next to the door where you should already be. If you take the shot right, Snake should say 'Good', or something similar. For your second photo, stand behind the crowd of Marines so that RAY is directly in front of you, and take a picture. The third shot is exactly the same as the first one, except from by the door on the left side of the room. For the 'Marines' logo, sneak back up past the guard near the pole and into the corner, next to the pole. Look up and you should see 'MARINES' written on RAY's leg. Take a photo. Try to take all the photos before the timer runs out. Finally, head back towards the right hand door and use the white computer in the corner. Otacon will view the photos. If you missed one or they are not sufficient, he will send you to take another one. Once all four are taken, watch the cut-scenes.
If you used the upper level way, slide down the pole and sneak past the guard, then take the photos.