This guide details all the areas that I personally think are secret. If a level doesn't appear on the list then it is because I feel there aren't any secret areas on that level.

Suggestions? Have I missed something? Made a mistake?
Leave a comment and I'll look into it!

Medbot hatch, just like in vanilla. Near the underground bunker area there are two small containers, a 10% lock strength hatch contains a medical bot for use. This is the only medbot on the island now (excluding the one in UNATCO) since the one near the docks was removed.




Sunken ship at the other dock. Another one from vanilla, well known. The ship has a 20% lock strength or 50% damage strength. Inside is a sawed off shotgun, reload mod, and accuracy mod.




Nanokey behind comm van. Same as vanilla, but not as well known. There is a nanokey for the satellite hatch hidden behind the comm van at UNATCO.




ATM datacube. Pretty obvious but included anyway, going through the vents in the statue leads to a room with a desk inside. A datacube can be found inside with the account details for the ATM as well as a PS20 and medkit.




Hatch near sniper. New one for the mod! The new sniper to the right of the spawn that's located on the crates. Under the large crates beside him there's a panel that isn't selectable. If broken a medkit, 30.06 ammo, range mod and prod charger can be found. The prod charger doesn't appear on realistic.




Crate by UNATCO. Another new one, by the entrance to UNATCO there's an opened crate, inside it an accuracy weapon mod.

Alex's floor panels, same as in vanilla. Two parts of the floor can be lifted to reveal a hidden area. Contains darts, tranquilizer darts, flare darts, soy food, cigarettes, two flares, and a key for the level 1 office doors.




Alex's cupboard. Including it anyway since I don't know how to find the code. The code is 2001. Inside is a lockpick, biocell, four flares and binoculars.





Behind the picture in Paul's office is a prod charger.

Crates in the water right where you spawn, containing a medkit and lockpick.




Castle Clinton's safe. Hidden behind a locked door with 20% lock strength and 50% damage strength is a locked safe, the safe is 40%/50% but there's a key for it on the terrorist downstairs. The safe contains an augmentation canister containing aqualung and environmental resistance. Also in the room is a key for the kiosk doors on the surface, a medkit, napalm and rockets.



At the end of the dock near Castle Clinton is a crate containing either an accuracy weapon mod (not on realistic) or a reload mod (only on realistic)

Area above shop by Smuggler's. On the roof of this locked shop there's a scope mod and 10mm ammo.




New building containing the basket ball court. At the top of this building there's two rooms, in the one nearest the elevator there is items in it. The items include a LAM, a crowbar, a pistol, 10mm ammo, 30.06 ammo, a lockpick and 50 credits. The lockpick only appears on hard or realistic. The 10mm ammo or 30.06 ammo doesn't appear on realistic. The LAM doesn't appear on hard or realistic.
In other room is a crate containing darts and a medkit.




Under the table in the park is a key for Osgood & Sons.




On top of the Ton hotel are some wooden planks, jump across them to reach the nearby building's rooftop. When on there climb across the plant beds and break open a window. Enter to find a small room with a desk, inside the left hand cupboard of the desk is a biocell. This room only appears (I think) in patch 1.0.1.4+ (unreleased as of 10th of December 2015).

Mirror near Smuggler's bed. Behind the bed there's a keypad, the code is 432, which moves the mirror. Behind the mirror is a medkit, clip mod, thermoptic camo, and a WP grenade when playing Biomod.

Paul's secret cupboard. Pretty obvious, keypad is behind the painting in his room and the code is 4321. Inside is a lockpick, biocell, medkit, ballistic armour, multitool, 10mm ammo, pepper cartridge and candybar. The lockpick and multitool don't appear on realistic.

The small room at the end of the bridge has a new place with pipes in it, there are crates next to it. In the crates are a lockpick and a medkit.




Armoury. Code to the room is 007. Contains buckshot shells, a prod, a gas grenade, an EMP grenade, a scramble grenade, a medkit, rockets, a prod charger, a LAW, 10mm ammo, WP rockets and two sets of 7.62mm ammo.

Under the generator there's a room with a safe inside. The safe contains an augmentation canister containing speed enhancement or walk silent. Also in that room is 2 LAMs.
The room filled with gas next to it also contains a lockpick, 10mm ammo and rockets.




Opposite where Jock lands there's a section of a building with two smoke stacks on it, there is a boarded up hole which can be broken. Inside is a terrorist with an assault rifle and a 20%/INF trunk containing a medkit, gas grenade and 7.62mm ammo. The medkit does not appear on easy.




Under that area is a window. There is a ledge near the window that can be walked on and broken to enter a new area. This area has a biocell, lockpick, flare darts, buckshot shells (not on realistic), 10mm ammo, 7.62mm ammo, and tranquilizer darts.

Same as before, the fake floor panels in Alex's room. This time containing a scope modification.





Behind the picture in Paul's office are some tranquilizer darts.

Same as before, two crates in the water at the dock. Medkit and lockpick.

On the upper level at the end of the tunnel (not where El Ray is) is a map. The map can be opened to reveal a datacube with relevant information and three flares.

Go to the locked rest room and then go back. When you go back around the bend there should be a cave in with a small opening in the corner. Inside that opening is an armed LAM, a biocell, a medkit, an EMP grenade, 4 flares and 38 skill points.




In the new train in this area in the end that's caved in there is a accuracy weapon mod and a range weapon mod. The range mod doesn't appear on realistic.

The pipe at the start next to the crate and crowbar has an EMP grenade in it.




When you find the barrel of ambrosia go up the stairs to the left, go to the balcony and look left. There is a locked door, enter it and look at the plant inside. Behind the plant is a button that opens the bookshelf next to it. Inside is 75 skillpoints, a knife, darts, a pistol, buckshot shells, range weapon mod, augmentation upgrade canister, a LAM, a prod charger and a LAW.
The pistol and augmentation upgrade canister don't appear on realistic.
The LAM and LAW don't appear on hard or realistic.




On the other side of the room containing the ambrosia is another hidden bookshelf. Go up the stairs to the area with the pool tables and pinball machines. Using the pinball machine closest to the bookshelves will open the secret area. Inside is ballistic armour, a lockpick, a medkit, and 501 skillpoints.
The lockpick and medkit don't spawn on realistic.




Near the exit to the elevator is a ladder, climb up it to get onto the roof of the room with the ambrosia inside, where the glass roof is. Up there are two vents which take you to a new vent area. On top of one of the computers in there is a lockpick.




Nothing to gain, but under the room with the augmentation upgrade canister is a room with a phone in it, hacking the computer will give you a phone number to call for a hidden conversation.

Item crates in/on the shipping crates. Same as vanilla I believe, looking around in the shipping crates can give you an accuracy weapon mod, a multitool and a lockpick.






Hidden area in the barracks. At the barracks near the dart board is a brick that can be pushed, inside is a key for the barracks dorms, 30.06 ammo (not on realistic), 7.62mm ammo, a knife, a mini-crossbow, a lockpick, a scope weapon mod (not on realistic), and a LAW.

Multitool in the cargo hold of the plane, hidden behind the crates.

Behind the picture in Paul's office is a clip mod.

New building containing the basket ball court. At the top of this building there's two rooms, in the one nearest the elevator there is a medkit in it.
In other room are three vials of zyme.

Mirror near Smuggler's bed. Behind the bed there's a keypad, the code is 432, which moves the mirror. Behind the mirror is a recoil mod, clip mod, ballistic armour, and a WP grenade when playing Biomod.

Paul's secret cupboard. Pretty obvious, keypad is behind the painting in his room and the code is 4321. Inside is 7.62mm ammo, darts, a lockpick and an augmentation upgrade canister. The lockpick and aug upgrade don't appear on realistic.




Inside Paul's wardrobe on realistic is where the aug upgrade is instead.




There is also a recoil weapon mod at the top of the elevator shaft.

The small room at the end of the bridge has a new place with pipes in it, there is a crate next to it. In the crate is 10mm ammo.

In the new building where the UNATCO troopers guard the 237615 keypad. Go inside and climb the ladder to the left, the go straight forward and outside. Climb the ladder there and jump up onto the vent pipe on the left. Follow the pipe, at the end look down to see a window with a ledge outside, jump into the ledge and break the window and enter.
Inside is a crate with a medkit (not on realistic), a crate with 10mm ammo, sabot rounds, an assault rifle, 7.62mm ammo and two TNT crates (one on realistic or hard). The TNT can be thrown out the window to destroy the robot near it.






In between the area with the railway and the robot guarding the tunnel are two electrical boxes, they both have 20% lock strength. The one closer to the railway has a biocell and multitool in it.




At the building to the left of the spawn tunnel is a keypad with the code 11011. Inside the building is recoil weapon mod and lockpick in crates. Along with a medkit behind the indestructible crates.

Inside the nanotech lab is a desk with a greasel dissection image. To the left of it is a vent. Inside the vent is a greasel protection ballistic armour and a plasma clip.

Same as before, the fake floor panels in Alex's room. This time containing 600 credits.

Both flight control decks contain a hidden compartment that uses the same textures as the walls with 50%/75% (10 min) strength. The compartment in Flight Deck 1 contains two biocells. The compartment in Flight Deck 2 contains a datacube and the key for all the barracks lockers.




There is also a sniper rifle hidden under the last bed in the barracks.

Right as you exit the helipad there's a building to the right which an officer guards. There is a keypad inside which has the code 22 but it's easier to break the wall instead. Inside are crates containing a baton and a sword. Up the ladder are a lockpick, biocell, prod charger, datacube containing the police keypad code, two pepper cartridges and a multitool along with 40 skillpoints.




Right as you exit the helipad there's a metal crate. Next to the crate is a wall with a different texture, right click it to reveal a ladder. Go up the ladder to receive 40 skill points.




At the right of the elevator to the helipad is a stair case, up the stairs is a medkit and 15 credits.




Beside this is another stair case with an ATM and two vending machines. Beside the ATM is a vent with a 20% lock strength. Inside is 7.62mm ammo and 10mm ammo.




Near the entrance to canal road is an unenterable shop, behind this is a path down underground. Going under here with make you find a murder. You will get attacked but will be able to loot the enemies. There is a lockpick on the beams in the area and there is also a carcass here with a datacube. (And in a future patch will have 100 credits)




Also near this on the surface is a building with breakable windows. By stacking crates and using the speed aug you will be able to get inside. Inside is two sets of throwing knives, 50 credits, 10mm ammo, a biocell, and a crowbar.




Face the entrance to the canal/Tonnochi Road near the lucky money. Turn around 180 degrees and leave out of the tunnel. Directly above you is a room with a breakable window, inside is a clip modification. (Requires a lot of stacking to get in)




In the same place there should be a shop with two women talking. Directly above that is a room with a LAW inside it. (There's nothing in the room above that LAW room)




Find the tunnel with a crashed car in it protected by two police and a barricade. Immediately to the right of that next to the trees is a path with a crate containing 10mm ammo.




Following the road where the crashed car is above is a zebra crossing. Follow it into the building on the left. Inside is a crate with 10mm ammo and a lockpick on one of the broken beams at the top.

As you enter the map from the market there's a white/grey building on the left. Go to the other side of it and look up, inside the windows is a room. Entering the room will give 15 skillpoints, two biocells, two LAMs, and two EMP grenades. (I don't know a way of legitimately getting up there)




When leaving the compound there's a building to the right with breakable windows on the top. There's nothing in there yet but there probably will be in the future. You can enter it by jumping around with the speed aug.

After getting the key from the compound for Jock's apartment go down the street and go right. There should be an elevator there which you can go up. Jock's room is on the 3rd floor, use the key to get in (or jump from the window of Maggie's apartment to Jock's balcony). Inside you can find his unique weapon, a silenced pistol, along with a sawed off shotgun, sabot rounds, a WP grenade on Biomod, a medkit and a lockpick.




Go back to the stairwell of Jock's building and go up the top to the ladder. Go up and look to the edge. Jump down onto the beams and then look to the left, there's a ledge. Jump onto the ledge to find 30.06 ammo and a sniper rifle.




Continue from above and go forward, climb the beam and cross to the other side (speed aug may be needed). Jump onto the ledge and go left, fall down onto the next ledge repeatedly until there's none left to go to. From here jump onto the billboard to find a biocell and lockpick.




Opposite the elevator to Jock's there is a small area. Inside one of the small cardboard boxes is a multitool




Above the first cover you go under at the start of the map is a room with an augmenation upgrade canister in it. The windows can't be broken so you can't access it, but it will probably be changed in the future so I'm including it.

There are assault rifles, gas grenades, hazmat suits, swords, lockpicks, darts, and tranquilizer darts to be found on the bodies in the tunnel by the police if you go there before you go to Versalife.




There is a flamethrower and multitool on the pipes in the room with the pipe to Versalife.

The freezer of the Lucky Money contains a LAW, tech goggles, 30.06 ammo, a sniper rifle, a biocell, and rockets.




The police have a new area outside the Lucky Money. Inside it is a 20% lockstrength wall hiding ammo. Inside there are two clips of 30.06 ammo (one on realistic), buckshot shells, and sabot rounds (not on realistic).




There is now an augmentation upgrade canister hidden under the bridge of Max Chen's room.




Max Chen's room has a bedroom to the right of it now, inside is a recoil weapon mod and 500 credits.

The platform to the big wooden ship leads to a room with two lockpicks in crates.




Using the paper lantern at the back of the big wooden boat reveals a biocell, repair bot, 30 skillpoints, 450 credits and four vials zyme.




The metal ship behind the wooden one has a hatch full of poison that contains rockets, napalm, and a plasma clip.




Go to the Old China Hand bar, which can be found if you go left immediately if coming from the market. Once there go into the back to the freezer section. Jump up the props and go into the vents, you'll go across the canal and to a ladder full of water. You'll need to go into there to find a body with the upgrade canister, but beware of the baby karkians swimming about!




Same place as above, but instead of going left to find the body, go right inside. You'll find a collapsed tunnel with a car crash. Crouching under the pillars and rubble gives you 10 skillpoints, 30.06 ammo and a laser mod.




Under the bridge near the Old China Hand bar in the water is a small tunnel. Go into the tunnel and go underwater, look for a small opening on one of the walls. Go inside it and go down, keep going and you'll find two rebreathers.




When leaving Versalife's UC through the pipe go left, you'll see a dock that you can climb on. At that dock is a room you can go in, inside is a pistol and some WP rockets.




When leaving the Old China Hand via the stairs look for a bridge, go over the bridge and down the stairs to find a room. Inside the room are some flare darts.

The painting at the elevator isn't solid, jump inside to find 7.62mm ammo, 10mm ammo (not on realistic), 30.06 ammo, range weapon mod, recoil weapon mod, and a reload weapon mod (not on realistic).




In the police area with the reflective glass near the security computers is a button, activating it reveals a room behind you. Inside is an assault rifle (not on realistic), mini-crossbow, two packs of tranquilizer darts, two packs of buckshot shells (one on realistic), 20mm HE ammo (not on realistic), a LAM (not on realistic), a gas grenade, an EMP grenade, and another security console.

There's a stealth pistol on the left hand side of the statue.




Go past the statue and to the right, then go into the bathrooms and find a grate. Go up the grate to find a greasel in the vents and gain 50 skillpoints.




Go past the statue and to the left. You'll find an elevator which leads to a room with a MiB and a key to the magnetic augmentation chamber.




There's an unselectable hatch on the statue near the stealth pistol, there is a datacube and two biocells inside.




Go to the barracks under the statue and go up the staircase on the right. Enter the vent at the end and go forward.
Go to the end of the vent and take that route to find an augmentation upgrade canister.
Take the route that goes up to find a new area. If there use the speed aug to jump on the vent to the left and find a range mod and silencer mod near the light. Also in this area is a repair bot, a lockpick in a crate (not in realistic), and two TNT crates.






Also in the barracks are two crates containing 20mm HE ammo and a GEP gun, the cardboard boxes also contain a hazmat suit and a rebreather.

Breaking the grate on the stairs to the UC and then going inside the vent will give 50 exploration skillpoints.

New building containing the basket ball court. At the top of this building there's two rooms, in the one nearest the elevator there are two gas grenades in it (one on realistic).




At the crates at Smuggler's back entrance are an augmentation upgrade canister, WP rockets, 20mm HE ammo, a LAM and an EMP grenade.




There is a datacube and range mod hidden in the back entrance to Osgood & Sons.

Mirror near Smuggler's bed. Behind the bed there's a keypad, the code is 432, which moves the mirror. Behind the mirror is a pepper cartridge, thermoptic camo, sabot rounds, 20mm HE ammo, a medkit, and an auto mod when playing on Shifter. The medkit doesn't appear on realistic.

Paul's secret cupboard. Pretty obvious, keypad is behind the painting in his room and the code is 4321. Inside is 10mm ammo, a multitool and a biocell.

The small room at the end of the bridge has a new place with pipes in it, there is a crate next to it. In the crate is 10mm ammo.




In the rubble when playing Shifter you can find the ILAW.

There are trailers at the gate at the start that contain darts, 7.62mm ammo, and a medkit (not on realistic).




There is a dead Russian agent on the top of a block of pipes outside the armoury. Beside her is a sniper rifle, 30.06mm ammo, and a datacube.

There is a GEP gun and 50 skillpoints on the front of the ship




There's a new hatch to enter through to bypass the guard and door if you come in through the door.

Jumping on the bilge pumps to the balcony takes you to a small armoury, inside is a lockpick, a plasma clip, a GEP gun, a scrambler grenade and an augmentation canister containing cloak and radar transparency.




Find the section with three spinning fans in one place and look for a vent near them. Go through this vent all the way to the end. You will find a dead sailor with a datacube. The sailor has a LAM. In a later patch he will also have a crowbar and medkit.
Climb up the ladder where he is to find a room containing a reload modification, 30.06 ammo, a pistol and sabot rounds.




By the electrified generators at the top is a room, filled with boxes and flares. Inside the cardboard boxes are credits, a candybar, a pack of darts, and a LAM

The tomb closest to Dowd can be opened to reveal a passage with a lockpick and medkit in it.




There's a door under the stairs of where Dowd is which contains 10mm ammo.




This whole crypt section is new. I won't spoil it but it's not for the faint hearted. Key is by the dumpster.

In Aimee's room there is a beam that has fallen, going up it reveals a lockpick, medkit, and scrambler grenade.




Sending the elevator up while in the building reveals a vent which contains a lockpick, crowbar and hazmat suit.

In the building across from the catacombs entrance you can find a phone. Answering it lets you receive a phone call from a special someone.

The weapons dealer can be found across the street from the bakery. Inside is 100 credits, 30 throwing knives, an assault shotgun, an accuracy weapon mod, a range weapon mod, sabot rounds, 10mm explosive ammo when playing on Shifter, rockets, a datacube, a laser weapon mod, a clip weapon mod, 30.06 ammo, a plasma clip and a plasma rifle.




Above the bakery is another room, on the balcony of the room is a crate containing a multitool, along with 200 credits, a medkit and a datacube inside.




On the main road is a building that can be entered, inside are two scrambler grenades.

The fireplace in Nicolette's room can be moved by interacting with the skull on it to reveal a vial of zyme, a lockpick, a plasma clip, a clip mod, and thermoptic armour.




The fallen wooden beam in the bunker can be climbed to reveal a lockpick.

A light fixture can be used to gain entry to the computer in the cathedral.




A grate can be found to the right of the gate at the start under some bins. Under it is a sewer which reveals a biocell, 20mm HE ammo (not on hard or realistic) and 50 skillpoints.

A key can be found in the bathroom behind a potted plant for the aquarium. Inside the aquarium is 50 skillpoints, darts and a rebreather.






The yellow generator at the helipad has a hatch on the side of it containing a biocell and multitool.

Behind the command building a sniper and MJ12 troop with an assault rifle can be found on a tower. Climb the tower to the top and climb over the pipes to find 75 skillpoints and two LAWs.




If you go over the wall behind the command building you will find a dead scientist with a biocell and two flares.




Enter the lobby and then the vent behind the desk. On the left should be another vent, going through there will lead into an area with water and a dead mechanic, the mechanic has a rebreather and a pistol.
Alternatively, jump off the building with the ladder beside the water area to get inside.

At the bottom of the flooded stairs is a door with the code 2134. Inside is a lockpick, augmentation canister, pistol, gas grenade (in a future patch), and ballistic armour.

The roof of the gas station can be entered to reveal a sawed off shotgun, binoculars and 50 skillpoints.

A vent can be found in the main building on shore, which leads to a hidden room containing a LAM and napalm.




A new armoury can be accessed from where the keys are held in the yellow building on the surface. Inside the armoury is a medkit, two crates of 10mm ammo (one on realistic).
Past the door under the stairs are also some buckshot shells and a gas grenade.




A sewer drain can be found at the beginning of the level to get you past the gate. The forklift can be used along with fall damage to break the wooden planks hiding it if you don't have the muscle augmentation to lift the crates out of the way.

Opening the sub-bay doors at the spawn and then leaving and going right in the water will lead you to a part of the base with a hole in it. Inside it is a body with a prod charger and a biocell, along with 200 skillpoints, a key for a lot of doors, a clip mod, and a GEP gun.




Between the spawn and the location above is a hatch that can be opened to reveal crates with rockets and a rebreather.




Swimming out behind the building with the green beacon will show a destroyed flooded room. Inside this room is a dead body with two biocells (and also an augmentation upgrade canister in a later patch), the locker also contains an accuracy weapon mod, tranquilizer darts, and regular darts. There is also a reload mod inside.

Using the vents by the elevators will take you up to an area with a glass floor. Around there is a dead mechanic with a multitool and lockpick next to him.

The building nearest to the silo with the walkway has a keypad on the top floor with the code 12. Using it reveals a staircase with a biocell, medkit, LAM and LAW in it.

In the hangar with the two MJ12 commandos and the MiB there is a fallen metal beam that can be climbed to find a dead mechanic. There is a key next to the mechanic that can be used to open a hatch in the Command 24 building which is to the right of the blast doors. Inside the hatch is an armoury containing a rebreather, LAW, ballistic armour, rockets, a datacube, a biocell (not on realistic), an augmentation upgrade canister in a safe with the code 9378, a candybar, and two flares.






Fall into the area with the fan in the hangar to land in water. Follow the watch to an are with a giant fan and a dead soldier. The soldier has an assault rifle, scrambler grenade, and laser mod.




To the right of the spawn is a building with a vehicle inside. Jump inside to find a dead commando with a biocell, EMP grenade, 50 skillpoints, and rockets.

In the maintenance access tunnel where the robot patrols is a dead scientist with a crowbar and LAM.




Entering the recreation area and going right at the lobby will show a vent on the wall which can be climbed in. Going up the ladder will take you up to near sector 3's access with a good sniping/hiding point.

Using the speed aug to jump over the area where the MiBs and GEP gun soldiers come from after you talk to Helios will find you 7.62mm ammo, a medkit, and 50 skillpoints.




A dead mechanic can be found on the roof of the building at the top of the stairs. He has 10mm ammo, a pistol, a biocell, and a datacube.

On the floor filled with the transgenics is a blue fusion reactor, with a door next to it. Enter the door and go into the room and open the hatch inside. Dive in the water and follow it. You'll find two deep chambers at the end.
The first one has a dead mechanic at the bottom with a multitool and biocell.
The other has a dead soldier with tech goggles and a LAW at the bottom.








In the area where you flush the system is a small room protected by two soldiers that contains a vent and ladder. Going in the vent takes you to a room with a multitool in a crate.




Above the ground on the next level is a UC with a security bot next to it which can be activated. By the bot is an area containing crates with 10mm and 7.62mm ammo. Beyond that is a ramp that leads to a dead scientist with a datacube.

Suggestions? Have I missed something? Made a mistake?
Leave a comment and I'll look into it!