Sam Stone has entered the museum to rescue Professor Stein, who has information that will help activate the Time-Lock. Quinn's has informed sam that the professor will not upload the information unless he is been rescued. Stone finds the museum overrun with arachnids, and rushes to get to the professor before either are killed.
In the boiler room at the start — between the second and third big machines is a clip. Reward: Shells +5.
Just outside the boiler room — look to the left. Behind two boxes are some cobwebs hiding a passage blocked off with planks. Break the boxes and planks with the sledgehammer and collect the clip. Reward: Assault Rifle Bullets +30.
In the hallway that leads to the stairwell, heading towards the stairs — There is a room with half-closed shutter just before the stairwell to the left, it has a translatable plaque on the ground. Behind the column on the back right is a clip. Reward: Shells +5.
On the second floor just after the stairs — there is a door with a "No entry" sign beside it. You can walk straight through the door by going around the sign on the right, which will show a "Secret room found!" message. In the next room is a weapon. Reward: Double Shotgun.
On the balcony in a side room on the second floor — The third room on the rear wall has a shelf. Break the shelf with the sledgehammer. Behind it is a switch; push it and a "Secret door unlocked!" message shows up. Now head out the door to the balcony in the main hall and jump over the railing to run along the lip on the wall, then around to the other balcony. The third shutter will be slightly open. Crawl under it and the message "Speedrun secret found!" is shown, and a huge chunk of the level is skipped. Reward: Shortcut.
On the balcony in the main hall across from the left side — on the way to the partially open shutter (in Secret 5), there is a health pickup. Reward: Health +50.
After Sam picks up a cell phone — Just after you kill a Gnaar there is a short hall heading left with a small Sphinx statue. Look behind it to see a switch. Press the switch to move the statue and collect the pickup. Reward: Electricity +50.
Just after you see a Shotgunner — Head right into the passage he came from. There is a shelf with a box on top. Break the shelf with the sledgehammer and head into the hall, which will show the message "Secret spooky hall found!" A scene with a ghost Rodriguez plays, and then you can collect the weapon at the end. Reward: XL2 Lasergun.
Back in the museum before you drop down — At the point you drop down there are bricks on the left you can scale, then jump over to the left to get to the second floor. Run around to the other room on the right and pickup the armor vest. (You could have already picked this up under 5.) Reward: Armor +50.