Base near the Ruins.
A little island in the Northern PacificÖ
Into the Base.
Run straight for the small medipack left of the hole in front of you, drop backwards in the hole and slide/jump/grab the ledge with Secret #1, Ammo, drop down get some Flares down there and swim till you reach a shaft up with a closed trapdoor, follow the small tunnel in front to a lever and pull it to open that trapdoor, go up and swim S, go into a crawlspace to the right, follow to an outside area. To the left is a Sentry gun, shoot a Guard just around the crates right and go to the far side for some Ammo and a Jump switch on the wall, shoot the Dog that comes out of the door between the crates and enter after you took a Medipack from the top of the crates. A big luxurious Yacht (more like the Queens private yacht than a Navy one) is moored in this dock, go right and shoot 2 Guards around the containers, check the corners for Ammo and see the Revolver on the grating up in the far corner, go N and hop behind some crates to get the Ammo and go to the far N, shoot the Guard around the corner and get the Uzis he drops, get some Ammo in the corner and climb the yellow crate on N wall, jump/grab the grated walkway in the corner and jump back to the one over the yellow crate. Do a long run jump/grab to the 2 stacked crates S and jump to the high stack of crates; go behind them and down to get the Crowbar. Climb back up and go over to the front deck of the ship, get a small medipack and drop into the hole in lower front deck, open the Crowbar door.
Check out the yacht for all the Goodies to find and shoot all Guards, some drop some stuff, make your way up to the upper back end of the ship and find the trapdoor (small handle along S wall ceiling) and open it to climb up to the top deck, spoilers like a F1 car, get a small medipack and climb the top of the ship, from the E wing you can jump/grab up to the rail of the portal crane, go S and get the Laser sight in the corner, jump back to the ship and climb the back spoiler, run jump to the stack of crates SW and hop to the grating in the corner to get the Revolver. Jump back to the ship and onto the back spoiler again, in the SE corner about 2 squares from the side and drop on the back side of the ship, grab the lower edge and spot the broken grating below, drop/grab and get in for Secret #2, a pile of Ammo. Drop to the water below and go get some Ammo (SE) and a Medipack (NE). Swim into the passage SW, and go back to the outside area, shoot the Sentry gun and get the Ammo under it, to the docks and climb the yacht again, all the way to the spoiler on top.
Grenade gun, Shotgun.
From here you can run jump/grab the Portal crane from a bit right of the most N tip of the spoiler, into the open spot, climb in and go left for a Medipack, right to jump onto the E rail going N and jump/grab the walkway on N wall, get the Ammo in the back and drop back into the broken grating, slide down to a wide passage with a big gate, shoot the Guard and the Dog and get the Ammo, go into the SW passage (the door closes behind you, giving access to another room you get to later) and follow the stairs up, shooting all Guards and picking up Grenade gun, Shotgun and Ammo. Open the door on top and get some Ammo, see a Guard leaving the room below and closing the door to the Sub behind him. You can spot the Bike there too, run jump over the fence to the other floor, get a Medipack at the window (nice view) and climb up the crawlspace, follow to Secret # 3, Ammo (hold the Ctrl key till Lara stops moving, multiple pickups here).
Jump over the fence to the lower floor and go to the opposite side after you shot the Guard and Sentry gun; in the Ctrl room youíll find a Jump switch to open the big gate. Drive down the path to the passage with the stairs and find the new entrance there, use the Jump switch to open the big doors further in the wide passage, drive in and right, down over a Guard and stop at the door to the right, get some Ammo on top of the crates (behind the crates in the NW is a hidden door) and find the Crowbar door NE, open and enter on foot. Go left and get a flyby of this big bridge room.
The Bridge room.
Thereís a bridge from left to right, with a climbable pillar below, you canít reach it from here, look down right and see a triangular ledge, jump there and do a run jump in N direction (diagonal over the small ledge), with a right curve in the end so you can grab the sloped wall past the deep centre part and hang on the edge, go left to the centre of the 2 squares, so when you backflip, youíll land on the tip of the light grey sloped block on the N side of the pillar, immediately jump into the passage and follow up ( to the left in the beginning is a grey closed door youíll get to later), shooting Guards and picking up Ammo and such, follow all the way up N to an outside area where you can climb into a crawlspace in the NW, go up to the top of this place and through the crawlspace in the SW, open the Crowbar door in the new area and throw the lever to open a trapdoor, go in and shoot the Guards, collect all Goodies and open the W door, use the lever to change the position of the bridge to level B-2.
Return to the light grey door near the bridge room (right) go in and follow up to a dark shaft with a burner, where you have to shoot the Guard to get his Flares, grab the ladder in the shaft, go up and around the corner, get into the crawlspace and follow back to the grey hidden door behind the yellow crate. Familiar territory, get the Bike and drive it over the bridge to the N side, take a right into the store room, over the Dog and leave the Bike at the entrance facing W, get the Valve pipe just left of the entrance. Drive the Bike through the fences W and the wall behind them with some speed, so you wonít fall back into the pit, go left and leave it near the slope for now. Jump back over the burner pit using the slope below, drop/grab back from the edge and shimmy right to a lever, which will open a door above. Follow the dark passage past the lever, Ammo, and open the trapdoor in the end, to get back to where the bike is, jump over the pit again and go left. Enter the door and shoot some Guards to reach the lever that controls the bridge, throw it back to get the bridge to level B-1.
Go back to the bike, using the passage through the burner pit and up the trapdoor, drive the bike up the slope and to the bridge left. Leave the bike here for a moment and go S, open the crowbar door on the higher floor and go left, use the grated ceiling to go around and drop/grab the ladder on the pillar, go down a bit and backflip to the walkway behind, open the small door and enter a room with a suspicious looking corridor, you wonít die in it, itís a timed run.
Stand in front of the passage and sprint to the lower grating, hit "Alt", to roll under it and sprint on into the door, kill the Dog and throw the lever to open another door. Go back through the broken grating E and up the slope to where you left the bike, up the higher S passage and into the open door left. shoot Guard and Dog and also the Barrel in the back, get some Ammo left and crawl into the crawlspace created when the Barrel exploded. Follow to the end and throw the lever, a trapdoor opens in the other arm of the crawlspace, go up in that room and use the Jump switch to open the door to the Sub.
Go back to the bike and drive it over the bridge, stop on the other side and park it, open the small door and get the Ammo, go back and go up the shaft in the ceiling, find a ladder in an elevator on other side and grab up, shoot a Guard outside and open a Crowbar door in the concrete structure and shoot the Guard to get his Nitro canister, go out to the square and shoot the Guard on the roof, jump up the white roof of the Bridge room, down to the next square, go NW and in the corner is a room with a Dog and a small medipack, go out and go E, spot the ladder, climb up to the top right side and backflip/roll/grab into a passage behind, shoot the Guard, get the Ammo and go up the crawlspace in the corner, stand on the higher block above the burner and look NW, hop back so you land on the grey roof, grab the edge and pull up, backflip/roll/grab the other side.
Go left and up the walkway, backflip over the grey beam S and grab the edge, drop and immediately draw a gun to shoot a mean Dog, look for a Jump switch in the dark (lowers a block in a sloped passage to the bike) on the pillar and go left and into the sandy area, climb the dark metal walkway and backflip over the N beam, drop to the square and find the sloped passage in the N, go down to the bike and get into the crawlspace in the ceiling once more. The elevator is on top floor now, so you can go below, enter the place where the ruins are, you get Secret # 4. Shoot Guards, Dogs and explore the whole place for Goodies, then go down into the hole at the ruins and find the antique Crossbow in a vase, near the dead Guard. Climb back up and go into the NW corner from the elevator, in this warehouse you can climb a dark crate in the W and go over to get back in the B-2 level, go to the burnerpit and drop in, grab the crack and go up the passage to the bridge and the bike.
To the Sub.
Go up the sloped passage to the square and straight to the corner passage, stop outside and fit the Nitro and Valve pipe to boost up the power, go up the stairs on foot and shoot 2 Guards in the upstairs room, get the Medipack and look out where the fence is, you have to jump over the square and the opposite wall into the next square, so go back to the bike, Save and from the bottom of the stairs hit the sprint key and jump over the square. Run over the Guard there and go into the Submarine docks. Shoot the Sentry guns if you like and you can also run the bike up the Sub, because the level ends here.
Never could find the 2 missing Secrets.