With the death of Professor Stein and the defeat of the Adult Arachnoid, Sam manages to get hold of Professor Stein's research on hand. Sam has been informed that an extraction helicopter is ready to pick him up, so he heads through the streets to find a suitable landing zone at the Ibn Tulun Mosque so that he can escape the city.
The sniper's perch (identified with many sandbags and Cloned Soldiers on it) nearby the starting area — Jump onto the nearby dumpster closest to the with sandbags, and then jump on the nearby utility box propped against the wall, and make another hop onto the top of the wall from the utility box. From there, jump over, or go around the sandbags to pick up the hidden ammunition. Reward: Shells +10.
In the yard after the sniper perch — there's a dumpster on the right. Jump on it and over the wall and pick up an armor helmet. Reward: Armor +10.
Before the overpass — The ruined building on the right can be climbed into. On the right hand side is some health. Reward: Health +11.
Just after the overpass — on the left are a bunch of shells. If you turn around — concealed by a column supporting the overpass — you will note a pill bottle that counts as a secret and spawns a Kleer Skeleton. Reward: Health +1.
Just after the overpass — On the road to the right there is a building on the right that is blocked off with planks. Break them with your sledgehammer and collect the pickup. Reward: Electricity +50.
Before the popup Cloned Soldiers — After the first overpass and before passing under it a second time, in the building on the right is some armor. Reward: Armor +10.
Under the overpass — Continuing on past secret 4 and beyond a ruined car is an armor shard that counts as a mini secret and spawns a Kleer Skeleton. Reward: Armor +1.
Beside the overpass — Just after passing under the overpass a second time, turn right and in a little alley is a weapon. Reward: 12 Gauge Pump Action Shotgun.
Beside the overpass — Just after passing under the overpass a second time, jump on the garbage bin and over the wall. Once you reach the barrels on the other side the message "Secret flanking performed!" shows up. This takes you around a small fight. Reward: Alternate route.
Beside the overpass — A building beside the overpass is blocked off with planks. Break them with the sledgehammer and collect the pickups. Reward: Armor +25, Shells +10.
Don't have a party without me — When Sam makes this comment, climb up the stairs until there's a break in the wall back towards the overpass. A health pack is hanging off it; jump across. Reward: Health +50.
Near the archway — Before the archway behind a barricade is ammo that counts as a mini secret. Reward: Rockets +5.
In the courtyard with three broken columns — There is a stack of boxes. Jump on them then over the wall to collect the weapon. Reward: M29 Infantry Assault Rifle.
Before the mosque — Along an alley just a bit before the mosque is a white wall with turned-over gray couch under a dark metal sign embedded in the wall. On the leftmost portion of the same wall past a two chair, and mattress will be a drum (the cylindrical container), jump on it, and look directly through the small hole in the wall. There will be a small electrical box directly in sight; shoot it and it will say "Secret door unlocked" meaning a speed-run secret was unlocked. Head to the nearby mosque entrance. Along the left side of the mosque wall prior to the stairs will be a large group of boxes. Break them to expose a ladder ("Secret speed-run found") which leads to the end of the outer mosque area. Reward: Shortcut.
The outer mosque — Around the second corner of the outer halls of the mosque is a stack of crates. Hidden among them is an armor shard. Reward: Armor +1.
The inner mosque — There's scaffolding on the building in the center. Crawl under it and then to the top, then jump up to grab the helmet. Reward: Armor +10.