If you arrive at the end of the level missing secret #3, it's possible to obtain it using the crawling corner bug. From the edge of the pit with the eviscerated corpse, enter the room on the right with the other mutagen pool and floating corpses.
There's an opening high on the far wall, above and to the right of the barred window. It's too high to reach by jumping, but you can get up there using the crawling corner bug.
Stand facing the wall below the opening, with Lara's left foot a bit to the right of the corner, as shown above.
Pivot about 45 degrees to the left to face the corner.
Hold the Duck button to crouch. Then tap forward once so Lara moves onto her hands and knees. You'll notice Lara's torso clipping through the outer corner of the block.
Release Duck and she should pop up into the doorway. (In case you're unfamiliar with this technique, the crawling corner bug is detailed on the Useful Bugs page, where there's also a video showing how to do it.)
Kill the 2 mutant creatures running around on the beach below. Then climb down the block steps to the beach.
You can then deal with the 3 remaining mutants. Two appear when you take either of the large medi packs sitting on the grates, and another mutant comes down the block steps when you jump up the slope into the cave with secret #3.
Inside this cave, avoid the toxic pool below on the left and pull up through the shimmering mist onto the ledge directly ahead.
Grab the rocket lying on the floor.
Take a running jump to the ladder on the left wall.
Climb down until Lara's hands are two rungs below the top of the sparkling vapor.
Then press Jump to backflip over the mutagen pool into the alcove behind. Pick up another rocket.
NOTES: If you don't yet have the ROCKET LAUNCHER, you'll get it here instead of the third rocket. The main walkthrough includes an alternate method for reaching this rocket.
To get back up, take either a running or standing jump from the alcove to the ladder.
Climb up until Lara's feet are one or two rungs above the the surface of the sparkling vapor.
Then press Jump to backflip onto the ledge where you started.
Turn right and carefully make your way up the stairs, jumping across various gaps with toxic goo below. You'll find another rocket and flares on the way up.
When you reach the top of the stairs, the chime should sound, and this secret will be entered into your stats. Return down the stairs and drop down on the right to get back to the beach. Climb the block steps and proceed to the level exit.
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