Sam Stone is en route in a helicopter to the museum in Cairo to protect a professor whose security detail has lost contact. Professor Stein is believed to have translated texts that could help activate the Time-Lock, mankind's last hope to defeat Mental's Horde. Stone's helicopter is shot down over the city, and he makes his way through the winding streets to the museum.
Use the Gnaar's eye — As soon as you melee the first Gnaar, look across the roof from where she came from. There's a green speck two buildings over. Throw the eye at a high enough arc (standing at the edge, at the same level as the top of the tall building to the left) that it hits the speck and tosses it onto your roof. If you miss with the eyeball, you can try again with one from another Gnaar (don't run or change weapons while holding an eye, as it will cause it to vanish/drop). Pick up the shotgun and kill the next Gnaar, showing a "secret assistance!" message. Note that the secret doesn't register if you use melee/hammer etc. to kill the second Gnaar. Reward: Pump Action Shotgun.
On top of the starting building — Jump across to the roof with an antenna that is beside the door down; the sledgehammer is a "Parkour secret." There is no reliable way down, but try jumping for a window ledge to break your fall. Reward: Sledgehammer.
From the roof where you've picked up the sledgehammer in the previous secret, jump down to the lower roof and face the building you originally started the game on. You will see some caged balconies that have a small ledge you're able to jump to. Jump across to land on the second from the top, then face the building you've just jumped from — you will see balconies as well. Jump towards the left side of the middle (second from the top) balcony to grab a pickup (it might not be visible from the balcony you're standing on). Reward: Shells +10.
Just after you kill the first Female Gnaar on ground level — To the left you can see a glowing blue armor on the third floor of a ruined building. Jump on the boxes, then the garbage bin, then the kiosk. Press up against the building directly under the armor and jump straight up to pick it up; this is a "Parkour secret." Reward: Armor +25.
After the road where you fight a bunch of Female Gnaar — You walk through a ruined wall. Look to the right beside a garage. Behind a corrugated wall is a health pickup with a "Mini secret found!" message. Reward: Health +1.
When you get the call from Jones — You head through a building that has stairs to the right. Go up two floors (jumping over the ruined stairs) and walk out to the balcony. Pick up the shoes. Reward: Serious Sam Classic outfit.
On the first main road containing a Beheaded Rocketeer — Behind the bus stop is a stone wall coming out from a building. Walk around it to the left and you will see a gap in the wall concealed by a bush. Go through the gap to pick up an electricity pack. Reward: Electricity +50.
When a warship blows up a building — After the fight, head through a broken section of wall and into an area with garages. Look to the left behind a bin to see a wall with uneven bricks. Break the wall with the sledgehammer and head on through to find many posters with special text and the message "Secret Yard of Fame Found!" Reward: Easter egg, Armor +25 at the end of the yard.
It is possible to get secrets 11, 12, 13, and 14 (in that order) if you don't accidentally fall off the wall or roof (if you do fall, you'll have to circle back around and enter the secret yard here in Secret 11). In the street before the parking lot — On the left hand side you can see a decrepit truck through a gate. Jump on the barrel behind the garbage bin, the bin, then over; "Secret yard found!" message pops up. Pick up the helmet, which will spawn some Kleer Skeletons. Reward: Armor +10.
In the alley beside the parking lot (in area 8), head back toward the gate you jumped over to enter the secret yard and jump on some boxes on the left, then up on top the garage, heading left towards the parking lot. Note that you will pass Secret 14 before reaching Secret 12, but save that until later if you want to save a little bit of time. From here you will be able to see Secrets 12 (Shells on the portable) and 13 (one health on a building ledge). Run over the shipping container and jump over to the portable in the parking lot, and pick up the shells. Reward: Shells +10.
When you're standing on the portable from Secret 12, look toward the building — you will see a health pickup on a ledge. You can jump on to the wall from here or backtrack and run along the wall from the building. Either way, follow the wall until it meets the building and then jump up to pick up the health (stay on the wall if possible to get faster access to Secret 14). Reward: Health +1.
Backtrack on the edge of the wall towards the where you came from, then head left, back towards the gate you jumped over to enter the Secret Yard. On the left will be a dark alley with some cells. Hop down and get the cells. Reward: Electricity +50.
In the parking lot — Jump on a car sticking out of the garages on the left, then hop down to between the garages. There is a clip down there. Climb out using the barrel. Reward: Assault rifle bullets +30.
In the plaza before the museum — where the helicopter crashed — there are several garages on the fare left. One of them contains a helmet. Reward: Armor +10.
After the final battle against the Kleer Skeletons — A message saying "Secret Arc de Triomphe enabled!" Head back to the ruined archway and walk through it. "Secret Arc de Triomphe enabled. Welcoming committee is arriving." shows up, and Beheaded Kamikaze spawn in.