Decided to try and make a list myself. This list will only include weapons and armor found during missions not mission rewards as you will always get those. It will also not include gunpart crates as they don't always have the same parts in them. As far as I know this is everything from every mission in the starting area. I have not gotten to the core missions yet so I will add those as I do them. If anything is missing please let me know and I will add it.

Shellguard Hub
Shellguard Backpack, Incident: FM-232 codex, Subject: N2-512 codex (In vent in east bathroom)

Shellguard medic helmet (In vent in med bay)

Train mission (Gunparts dealer)
No items (I don't remember any and this mission cannot be replayed so I would appreciate if someone could confirm there is nothing to be found there)

Hidden mission (Sword in stone located in upper east most portion of outpost up the mountain side)
Old guard Spear, Sword & flower statue (located on other side of maze end teleporter)
(it is also worth noting the protectorate flower is here in great abundance if you missed it in the intro)

Toy Arena 1&2 (Toy vending machine) and Arena Fights 1-5 (Fan standing next to arena teleporter)
No items

Arena fight 6 (Fan standing next to arena teleporter)
Praxis Imperium (Dropped by boss)

Lockjaw Training (Lockjaw&Vehicle dealer)
2x Shellguard Training Lockjaws

Vehicle Rescue (Lockjaw&Vehicle dealer)
No items

Mercenary Mission 1
No items (There is a protectorate flower up the hill past the exit teleporter if you missed it in the intro)

Mercenary mission 2
No items

Prototype Problems
Shellguard Plasma Claw (Dropped by boss)

Mercenary Mission 3
no items

Medical Mystery
Survivors Staff (Dropped by boss)

Colony Attack
Clown Mech Horn (In morphball tunnel in break in wall in Apex lab. The tunnel opens up into a cave with some crates and there is a second morphball tunnel above that requires the spike ball to reach. Horn is in the crates at the end of this tunnel)

Factory investigation
Ironwatch Helmet(At the base of the first elevator combat sequence there go right and there will be a morphball tunnel. it is in the crate at the end of the tunnel)

Ironwatch Torso Armor (After the power conduit take the elevator down and then go into the next room and climb up to the upper catwalk. There is a morphball tunnel above the door to the next catwalk section. It is in the crate at the end of the tunnel (not the 3 crates you first encounter the tunnel has a second section)If you reach the checkpoint you have gone too far)

Ironwatch Legs (There is another morphball tunnel in the observation room just above the exit teleporter. it is in a crate at the end of the tunnel)

Weapons Facility
Shellguard Bot Torso (There is a morphball tunnel in the area where you first encounter enemies above you in the building you come out of. It is in the crates at the end of the tunnel)

Shellguard Bot Head (After the shooting range climb up the other side of the wall of the door you use to leave. The crate will be on the antenna. If you go past the dropship you have gone too far)

Shellguard Spider Torso (Ihen you reach the locked door and go down in the pipes under the water there is a chest that can only be reached with the morphball. It is in there.

Spiderbot Legs (In the room just above the locked door there is a morphball tunnel at the far end of the room. The crate is on the other end.

Shelguard Spider Head (Above the locked door when you make it out onto the room there is a crate on the antenna on the far side of the roof above the turret activation switch)

Ironwatch Combat Wrench (just past the locked door in the room with all the consoles just above the door you enter through there is a crate)

Shellguard Heavy Bot Head (When you enter the courtyard with the small buildings with communications dishs before the fuel tanks there is a room on top of the building you just came out of with the crate in there.)

Shellguard Heavy Bot Torso (On top of the second fuel tank to the right)

Ironwatch Cutter (In the observation room above the exit teleporter)

Fortress Assault (Part1 Space&Cannon)
No items

Fortress Assault (Part 2Inside the Ship)
Shellguard Radio Equipment (On the path above the locked door once you throw both switches there will be a morphball tunnel to in the turret compartment to the right. The crate is at the end of the tunnel)

Shellguard Toolbox, Shellguard Monarch HBLAP, Veteran Chest (In the room after the sniper turrets with the large window there is a path that leads up on the left side of the room. There are multiple crates at the end of the path)

Ironwatch Lance (Just above the glass where you can see the 4 weapon crates there is a shadowed path leading up with a crate at the end)

Ironwatch Mace, Log Book 1-4 (When you take the mech again shortly after there is a path leading right. the crates are at the end of the path)

Shellguard Plasmite Staff (When you reach the end of the zero gravity area and climb the stairs there will be a fork. Go right and drop down to turn on the console and open the door the crate will be inside.)

Fortress Assault (Part 3 Core & Escape)
R.A.I.L. (Dropped by boss)

Ironwatch Saber (after the elevator and the upward firing beam you will enter a large room with an upper and lower path. The crate is on the lower path on a platform close to the bottom of the room)

Customized Rifle (in crate next to escape shuttle)

Find the Survivor

HBL-G Launcher (After climbing over the antenna there is a morphball tunnel at its base. The crate is at the end.)

Breaker Rifle (After the room with the large broken window just after the checkpoint climb up and this crate will be on the upper left almost directly above the checkpoint)

Heavy Equipment, Titan Helmet (After the room with the large broken window after the checkpoint before you enter the next room there will be a snow pile covering a pipe morphball tunnel. (the tunnel itself is not blocked) The crates are at the end of the tunnel.)

Thermocatalytic Launcher (just after assault drone fight in crate)

Cauterizer (just after going through the teleporter and going outside climb up above the door you came out of. There will be a small tunnel in the snow with the crate inside)

Praxis Salvos (dropped by the survivor)

Frost Hound (Just above the exit teleporter through the break in the roof in the prior hallway.)

Missing person 1-3 (Scientist at top of outpost)
No items (it is however worth noting Fire Bobots can be found 100% of the time on 1 and 3 will have a large number of base game unique weapons and cosmetics from the Apex pool)

Flight testing (Scientist at top of outpost)
No items

Rescue mission (Scientist at top of outpost)
Titan Broadsword (just before final room with console above you)
(this mission has a large number of unique base game weapon spawns)

fortress prototype rematch simulation
Airstrike Flare pistol (dropped by boss)

Fortress Core Remach Simulation
Fulcrum (dropped from boss)

Twin Drone Simulation
Typhoon Minigun, Boss Store (At exit teleporter)

Survivor Remach Rematch Simulation
Survivors Guilt (dropped by boss)

Test A New Transport Method Simulation
Flight helmet, Armored Flight Jacket, Flight Trousers, Mercinary breaker, Merchant custom, Gunmod Constructor (All in crates at end of level)
(It is worth noting that there are like a dozen rare pets that can be found here)

Praxis Champion Remach Simulation
Praxis Lockjaw (dropped objective boss)

Destroy the Seigebreaker (given by fortress core)
Siegebreaker (dropped by 1st boss)

Miners Diary (in room before teleporter next to checkpoint)

Quantum Wastelander (When you reach the sign that says Hazard next to the miners diary dig out the stone between the purple blocks and you will open up a hidden level. Go down and when you reach the first room with a shallow poison pool there is a tunnel in the upper west side of the room with a crate in it.)

Kalis Cannon (dropped by hidden area boss)

Alien Caster, Alien Rifle, Alien Spread rifle, Alien Heavy Rifle, Energy Barrier (In a series of chests in the room past the hidden boss)

Fight Chomby
Chomby controler (dropped by boss)

Falx Scope, Chomper Blade (in crates next to exit teleporter)

Strange request (man hidden in vents)
Swordfish Launcher(next to 2nd translation mural)

Marlin Launcher, Strangers Notes (next to exit teleporter)

Defeat the Miniknog
Rare base game items Internal Report #E86A & Miniknog Mech Body (this level uses the Miniknog space encounter as its base and contains both unique drops in the upper most part of the first section you enter though you must unlock the codex room from a console outside on the other side of the room the mech body is in a storage locker on the other side of the same floor. If you encounter a poison pool on your left at the base of an elevator you have gone too far. The chest in the pool contains one cosmetic item from the scientist set with other possible rare items)

Ironwatch Mine Shotgun (when you reach the sign that says ministry of knowledge just before it there will be an elevator down. Follow that tunnel unill you reach another elevator and go up and there will be a high tech chest)

Shattered Binding (dropped by boss)

Ironwatch Heat Carbine, Ironwatch Cryo Carbine (in tech chests next to exit teleporter)

Rail Defense
Hub Theme Player (After you finish with the turret jump into the nearist water and go right. It is in a chest about as far right as you can go)

Old Hub Theme Player (After you finish with the turret jump into the nearist water and go left. It is in a chest as far left as you can go)

Ironwatch Hammer SMG, Turretsmith Helmet, Harpoon Gun (In chests in teleporter room)

Old Guard Helmet (on the surface past the teleporter room climb the building it is on the roof behind the antenna)

Ocean Base
Fortress theme player (In water directly under starting location)

Old Gunship Theme Player (when you reach the underwater base go over the top and it will be in a crate on the far wall)

Hardsuit Snubnose, Birth of Shellguard (when you exit the first underwater base after the starting area go left and you will find a cave with a large statue and an arcade. The items are in crates in the arcade. If you reach the area with the lunar beds you have gone too far.)

Survivors theme player, Hunters Avarice (in the room past the lunar beds you will come across a broken catwalk with a lever at the top, pull that lever and climb back down and a door will have opened below the catwalk. The items are in crates in the opened room)

Meteor Grenade Launcher (In crate in hallway just before exit teleporter)

Crab Calamity
Prototype HBL (After the first jump just when you reach the first heat spikes dismount and go down. Item is in a crate in building. If you reach the giant robot you have gone too far.)

Ironwatch Gyro Launcher (when you reach the cliff with the locked door the item is in a crate at the top of the cliff)

Ironwatch Imperium (in crate in room where you unlock door)

Falcon Assault Rifle (When you reach the middle elevator climb the wall to the east that you come out of and there will be a small gap with the crate in there)

Ironwatch Hammer AMR (to the right at the top of the elevator shaft)

Valiance (next to exit teleporter)

Medium Mayhem
Fireman Helmet, Fireman Chest, Fireman legs (In the room with the Erchius crystals and fuel in a glass case on the ceiling to the left there will be a morphball tunnel it is at the end of the tunnel)

Gunship Theme Player, Hammer Hand Cannon(In the room with the Erchius crystals and fuel in a glass case on the ceiling to the right there will be a morphball tunnel it is at the end of the tunnel)

Ironwatch Hammer Rifle, Rampart MK1 (Next to exit teleporter)

Medium Mayhem 2

Tidal Toxin (In crate in room with tents)

Estoc HBP-AM1 (next to exit teleporter)

Travelling Merchant (mod creator) could not recall if the Shellguard Energy Shield, Laser Claw and Robust Revolver were implemented or not so if you find them please add them. The spawner also does not contain the current ironwatch melee weapons for some reason so I cannot be sure I got them all as well as any objects so please feel free to list anything I have missed. I have been unable to find the Reflek Sniper and Ironwatch Flame Claw but have been told they are implemented.

Awesome compilation!

But... I can't find anything after 'Fight Chomby'. Ocean Base? Rail Defense? Medium Mayhem? Where are all of these?

Originally posted by HoneyBun Pancake -TPF-:

Awesome compilation!

But... I can't find anything after 'Fight Chomby'. Ocean Base? Rail Defense? Medium Mayhem? Where are all of these?

The 3 irongaurd soldiers in the downstairs part of the core area. Stranger is in the vents past them.

how do I operate the vehicle in the Rescue Mission?

oh hey you missed an autocannon on the 3rd part of the fortress mission. its right after the elevator in the double room. its right above the door

Ironwatch FLame Claw: In Fortress Assault 2, right at the end in the big control room before the teleporter, there is a hidden nook in the upper left, almost above where you entered. The flame claw is in the weapons crate

Heavy Cannon and Composite chest: in the morphball tunnel past the escape shuttle in a zero gravity enviroment in the fortress part 3. I just noticed that one today

On the mission Fortress Assault (Part 2) after the zero g area and you climb a bunch of stairs. there is an area with a bunch of consoles. 6 large consols connect to 6 smaller ones and 12 mini consoles. if you turn them all on a wall moves to the upper far left of the room and you can find a iron watch flame claw.

On the mission Fortress Assault (Part 2) after the elevator in the first room just above the door there is a pipe to a chest with a HBL-HE autocannon in it.

What about the Blank Shellguard Helmet? I remember finding it somewhere, im pretty sure it was somewhere in the start of the storymode.