August 2023 Update: Now that a remastered Operation Alien Overlord is on the way with fresh recruits, I decided to create a combined guide out of the separate ones for the mission packs I did back in May 2021. Unlike the original's, the secrets for these campaigns remain untouched by the remaster. Thus this guide can be used either for classic or remastered runs of both. If need be, the original (separate) guides can be still be found here and here, respectively.
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Following the same structure set by the original, both The Reckoning's (MP #1 / Xatrix) and Ground Zero's (MP #2 / Rogue) singleplayer modes consist of five units of varying length and features a total of 102 (65+37) secrets. This guide has been created to serve as a clean-cut visual aid for new and returning players alike aiming for getting all of them.
As with all classic shooters, discovering the secrets by one's self is a huge part of the fun so it is recommended that you only refer to the guide to find out what you are missing instead of following it step by step. Though not marked as secrets, there are also many more items to be found in explosive crates or hard to reach spots so a thorough search of any given level is almost always rewarding.
Take heed of Ground Zero: due to this second mission pack being way harder compared to both the original and The Reckoning, you need those precious items more than ever.
The guide is laid out so that the numbering of the secrets is in line with the mostly linear flow of the game: where multiple paths are available, it is presumed that the player goes towards the objective first. In addition, due to the unit-based nature of the title, a few of the secrets are only accessible upon returning to the same level at a later stage. In those cases, a later visit to the level in question can be identified by the tag (Continued) besides its name.
Of the two shots provided for the secrets, the first one covers the area it is to be found in while the second one shows a particular detail, which, in most cases, is the trigger itself. Additional tips are deliberately kept short to let the shots speak for themselves.

Intended for classic players, as the remaster offers menu-based unit selection.
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Although not offered through the in-game menu, it is possible to start playing directly from a later unit with a loadout as seen fit by the developers. This can be done by using the following commands (given in italics):
THE RECKONING
Military Compound / exec xcompnd.cfg
Industrial Region / map industry, then exec industry.cfg *
Spaceport / exec xhangar.cfg
Moon Base / exec xmoon.cfg
(* The map command is needed beforehand for Unit 2, as the command to launch it in the following .cfg file has a double slash in front of it, thus the engine leaves it out as a comment rather than executing it - this must be an oversight on developers' part.)
GROUND ZERO
Base Complex / exec runit2.cfg
Research Hangars / exec runit3.cfg
Munitions Installation / exec runit4.cfg
Widow's Lair / exec runit5.cfg
Note that the game defaults to Medium difficulty unless it is changed by using the skill variable. To start playing on another difficulty, be sure to type in the appropriate command (given in italics) from the list below before executing the command for the unit.
Easy / skill 0
Medium / skill 1
Hard / skill 2
Nightmare / skill 3
In Quake series of games, difficulty levels differ in the monster count and the amount of damage taken by the player, so Hard difficulty is recommended for the most complete experience. As stated in the foreword though, mind that Ground Zero is notorious for its unfair encounters so (even if you are accustomed to Hard) you may want to start on Medium difficulty in case it is your first-run through the pack. Nightmare (also known as Hard+, as displayed in the status / objectives subscreen) difficulty, which was originally hidden and is otherwise the same as Hard difficulty, remains a matter of preference as it requires a different approach to the gameplay due to its highly reducing the pain states of the monsters as well as its making them quicker on the trigger.
It is already pretty well-known that the game, as in most of the classic shooters, allows loading of the levels directly by typing in their filenames alongside the map command. Still, since doing so does not grant the player any type of equipment (other than Blaster) nor any key items which may be required for progression, the filenames for the levels are purposely left out of this guide.

This unit consists of 3 levels that contain a total of 10 secrets.
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THE SWAMPS
1/3 - Dive into the water, make your way around and jump across the gap.
2/3 - Climb onto the rocks by the sewer entrance and check the pool in the cave.
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SEWERS
1/3 - Shoot the cracked part of the wall in the corner right before the slime tank.
2/3 - Shoot the grate in the water by the laser security grid.
3/3 - Dive into water and check underneath the security bridge after raising it.
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WASTE SIEVE
1/4 - Shoot the above button as you pass the tumbler to open up a compartment ahead.
2/4 - After getting out of the pool, turn around and shoot the Strogg symbol.
3/4 - Make your way to the top of the pipe room and check the dark corner.
4/4 - Drop down from the control room's windowsill onto the pipes below to reach the item.
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THE SWAMPS (Continued)
3/3 - Use the explosive barrel to reach the newly-opened alcove after extending the bridge.

This unit consists of 5 levels that contain a total of 15 secrets.
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OUTER COMPOUND
1/4 - Shoot the explosive barrels and push the panel behind them that slightly juts out.
2/4 - Shoot the damaged ceiling and climb onto the crates to reach the second floor.
3/4 - Shoot the button and drop down to the lower floor to reach the newly-accessible area.
4/4 - Shoot the button and get to the other side of the slope before it rises.
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INNER COMPOUND
1/5 - Climb onto the crates and push the button located on top of the computer.
(Needs to be done before activating the laser in the same room.)
2/5 - Drop down to the floor underneath the laser to access a hidden compartment.
3/5 - Jump and touch the blinking light fixture to open up another hidden compartment.
4/5 - Climb onto the rocks next to the bridge and make your way to the top.
5/5 - Dive into the water and look for a hidden cave.
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CORE REACTOR
1/3 - Crawl under the stairs in the machinery room to find a hidden item.
2/3 - Get on top of the pipe, go right and drop down onto the crate to reach the item.
3/3 - Get on top of the pipe, go left and drop down onto another crate to reach the item.
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THE WAREHOUSE
1/2 - Disable the force fields, shoot the button and drop down on top of the elevator.
2/2 - Jump in the shaft while the fan is still active to reach the ledge above.
(Needs to be done before blowing up the conduit in the same shaft.)
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INTELLIGENCE CENTER
1/1 - Download the data, climb the ladder to get the suit and dive into the acid below.

This unit consists of 5 levels that contain a total of 22 secrets.
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INDUSTRIAL FACILITY
1/5 - Jump onto the ledge and leap from block to block till the very end.
2/5 - Shoot the explosive crate then the button behind it to open up a hidden compartment.
3/5 - Shoot the same button once more while keeping inside the said compartment.
4/5 - Shoot the part of the grating above the light fixture on the duct to reveal a hidden item.
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OUTER BASE
1/3 - Shoot the button inside the vent to open up a hidden alcove ahead.
2/3 - Shoot the larger grate in the corner to access a hidden area.
3/3 - Take the elevator up, send it back down and drop down on top of it to find a hidden item.
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Easter Egg
An invulnerability power-up can be seen just by the tip of it on the upper ledges of Industrial Facility, right next to the Refinery entrance. Rocket jump towards it to receive a message from the developers. -- ChrisLP adds that it can be picked up if approached above from the pillar side, by doing another rocket jump that takes you over the trigger.
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REFINERY
1/3 - Shoot the explosive crate, push the newly-revealed button, take the suit and dive into the acid to find a hidden item.
2/3 - Take the suit near the marker receptacle, return to the previous area, dive into the acid and surface under the bridge.
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INDUSTRIAL FACILITY (Continued)
5/5 - Use the blue-coloured light fixture as a step and get on top of the crates to reach the item.
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WATER TREATMENT PLANT
1/7 - Use the semi-hidden steps that jut out from the rock to reach the top of the structure.
2/7 - Shoot the explosive crate first then make it to the item in sight by way of the others.
3/7 - Still in the same room, blow up the semi-hidden conduit and make your way to the ladder that comes down by jumping from crate to crate to reach a hidden area.
4/7 - Dive into the canal and check the narrow opening next to the floodgate.
5/7 - Dive into the canal in the following area, shoot the cracked grate and get into the pipe.
6/7 - In the area reached via swimming through the said pipe, dive back into the water but get into the other pipe this time to find one more hidden item.
7/7 - Shoot the grate at the end of the canal to find another hidden item.
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BADLANDS
1/4 - Check the sides of the hatch opening to find a grill, shoot both that and the button behind it then drop down back into the hatch to find a newly-accessible compartment.
2/4 - At the upper cliffs overlooking the hatch, work your way up to the ledge on the left.
3/4 - Still at the cliffs, this time work your way up to the ledge on the right.
4/4 - Work your way up to ledge next to the exit via the rocky steps and jump on top of the structure to get the item.
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REFINERY (Continued)
3/3 - Get on top of the pipes and shoot the cracked one in the middle to reveal a hidden item.

This unit consists of 3 levels that contain a total of 11 secrets.
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LOWER HANGARS
1/5 - Look around the crates in the corner of the storage area to find a semi-hidden item.
2/5 - Following the other path, shoot the wall with a writing on it to access a hidden area.
3/5 - Look for a striped panel after getting off the elevator and shoot it to reveal a hidden item.
4/5 - Shoot the explosive crate and the button behind it to open up a hidden compartment.
5/5 - Take the opening between the crates and shoot the explosive one under the stairs.
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THE HANGARS
1/3 - Jump on top of the red-coloured crate to find a hidden item around the corner.
2/3 - Check underneath the ramp that leads to the freighter to find another hidden item.
3/3 - Shoot the striped panel while crawling through the maintenance hatch.
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STROGG FREIGHTER
1/3 - Jump onto the crate right across the starting point and crawl in to reach a hidden item.
2/3 - Shoot the Strogg symbol at the back of the computers to reveal a hidden compartment.
3/3 - Shoot the button in the alcove to open up another hidden compartment.

This unit consists of 2 levels that contain a total of 7 secrets.
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CARGO BAY
1/5 - Get on top of the crates stacked in the corner and drop down into the opening.
2/5 - Get on top of the rafters, make your way to the end and shoot the Strogg symbol.
3/5 - Check behind the crates stacked at the back of the balcony overlooking the entrance.
4/5 - On the second floor ledge, shoot the wall with a writing on it to reveal hidden items.
5/5 - Shoot both buttons located way above in the circular room to reveal a hidden area.
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COMMAND CENTER
1/2 - Shoot the button above the reactor by the entrance to reveal a hidden compartment.
2/2 - Shoot the ice covering the puddle of water inside the cave to reach the item within.
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END OF TRANSMISSION: 'THE RECKONING' -- INCOMING TRANSMISSION: 'GROUND ZERO'

This unit consists of 4 levels that contain a total of 13 secrets.
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LOWER MINES
1/5 - Right at the beginning of the level, shoot the ore crystal to reach a hidden item.
2/5 - Activate the mover and shoot the ore on it once it reaches its destination.
3/5 - Activate the cart track and get on one of the carts to reach higher ground.
4/5 - Shoot the cracked floor underneath the gear to reveal a hidden item.
5/5 - Activate the crane and shoot the explosive crate once it reaches its destination.
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THAELITE MINES
1/4 - Shoot the cracked part of the rock in the alcove to the right while riding the elevator down.
2/4 - Shoot the ore crystal found in the corner of the tunnel to reveal a hidden item.
3/4 - Follow the cart track in reverse and jump down to reach a hidden area.
4/4 - Shoot the button located on the side of the pillar to reveal a hidden compartment.
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TECTONIC STABILIZER
1/4 - Shoot the button located behind the pipe to open up a hidden compartment.
2/4 - After destroying the wall nodes, open the coolant tank by using the nearby console.
3/4 - Look for a semi-hidden item on the pipe next to the secondary coolant tank entrance.
4/4 - Instead of running for the exit after disabling the pumps, return to the generator room and wait for a chunk of rock to fall down onto the pipe below. Jump across and drop down into the newly-formed hole to access the secret level.
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MINE ENGINEERING (Secret Level)
This level has no secrets. However, two items of note, the suit of body armor in the initial area and the shot of adrenaline in the next one are missable due to the rising lava.

This unit consists of 4 levels that contain a total of 11 secrets.
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EASTERN WAREHOUSE
1/4 - After disabling the track by removing the power core, check underneath the cargo cart.
2/4 - After obtaining the red key, reach the monster closet in sight by way of crates.
3/4 - After nullifying the electric current, dive into the water and look for a hidden item.
4/4 - Look for a semi-hidden passage under the slope in the area leading to the exit.
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WATERFRONT STORAGE
1/4 - Make your way to the area behind the explosive crate via the crates nearby.
2/4 - Drop down and jump onto the mover once it is activated to reach an item further on.
(Needs to be done in a single try since the mover does not return to its starting position.)
3/4 - Shoot the panel that slightly juts out to reveal a hidden compartment.
Follow your objectives to Logistics Complex and return to Waterfront Storage.
4/4 - After using commander's head, shoot the panel in the corner to reveal a hidden item.
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TACTICAL COMMAND
1/2 - Shoot the button near the ceiling upon leaving the shuttle to reveal another hidden item.
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LOGISTICS COMPLEX (Continued)
1/1 - Shoot the button located on the side of the terminal to reveal a hidden item.
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TACTICAL COMMAND (Continued)
2/2 - Dive into the water and shoot the cracked wall to reveal yet another hidden item.

This unit consists of 4 levels that contain a total of 9 secrets.
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RESEARCH HANGAR
1/2 - Shoot the button on the ceiling next to the pillar and dive into the water to find two items.
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WASTE PROCESSING
1/2 - Look for a broken beam above the door and shoot it to get the item residing on top.
2/2 - Just before activating the reactor, push the green-coloured panel on the side of the server to reveal a hidden item.
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WASTE DISPOSAL
1/2 - Right at the entrance, dive into the water and check the other side of the pipe.
2/2 - Still at the entrance, shoot the cracked floor near the dead marine to reach another item.
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MAINTENANCE HANGARS
1/3 - Right at the beginning, find the damageable part of the rock (shown already destroyed), shoot it to reveal a hidden area and receive a message from the developers.
2/3 - Shoot the panel (shown already shot) and reach the item using the explosive barrel nearby.
Follow your objectives to Waste Disposal and return to Maintenance Hangars.
3/3 - Get the suit, shoot the hidden button, wait for the third container in line and dive into it.
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RESEARCH HANGAR (Continued)
2/2 - Shoot the top part of the tallest server in the room to reveal another hidden item.
Easter Egg
Type the cheat command 'noclip' in the console before leaving the unit and look for a peculiar room outside the playable area which houses the word 'ZOR', the nickname of the level's designer, Berenger Fish.

This unit consists of 2 levels that contain a total of 4 secrets.
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MUNITIONS PLANT
1/2 - Shoot the cracked panel above and the button behind it to reveal a hidden item.
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AMMO DEPOT
Easter Egg
Look up in the entrance hall to find a grate on the ceiling and shoot it as long as it takes to receive a message from the developers. Shoot the newly-revealed button as much as needed to receive one more message from the developers. Mind that this process takes a lot of ammo.
1/2 - Activate the bio-maintenance chamber and enter the pod in the previous room.
2/2 - Shoot the bottom of the crate hanging from the beam to get a hidden item.
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MUNITIONS PLANT (Continued)
2/2 - Shoot the slightly indented wall in the gondola room to reveal a hidden compartment.

This unit consists of a single level that does not contain any secrets.
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WIDOW'S LAIR
This level has no secrets.
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END OF TRANSMISSION: 'GROUND ZERO' -- RETURNING TO LISTEN MODE

Intended for classic players, as the remaster is already a fully fledged source port in itself.
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All the screenshots within the guide are taken under the Yamagi client (build 7.45). It is a carefully maintained alternate executable that offers modern OS compatibility, a newer OpenGL renderer featuring enhanced visuals with external texture and proper widescreen support, a much better sound driver with surround capabilities and ogg playback, a reworked and more reliable save system and a scalable HUD alongside hundreds of code fixes and a bunch of subtle quality of life improvements. It is thoroughly recommended for a bug-free, hassle-free vanilla experience. Check it out here.[www.yamagi.org]
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Guides for the original, CotM, N64/PSX and Zaero following the same format seen here are also available to accompany this one. Check them out if you are in for a completionist's run: