A small fix, but a crucial one for progression:
-Fixed tot4's final button to the secret exit having a loose silver key requirement

Download link is the same.
Fixed a faulty trigger in tot5 where the cave tunnel at the start is sealed.

Download link is the same.
-Added a guide for all the campaign's secrets in the game files.

-on tot3:
*The doors leading to their respective keys lock players behind once they enter the respective silver/gold key region so players don't backtrack needlessly.
-on tot4:
*Changed a secret on level 2's gold key region to be a bit more explicit.
-on tot7:
*Fixed a faulty secret related to silver doors, which now only display a common message.

Download link is the same.
v1.031 comes with crucial fixes for tot4:

*Fixed the exit door not opening
*Fixed the way to the secret exit not triggering during the final sequence
*Fixed the multi-key door not displaying the correct locked message
*Fixed key signs at the start of each level not showing the correct key texture

Download link is the same.
Tomb of Thunder has been updated to version 1.03:

-Added Co-operative support.
-Chaingun rework:
*Removed the spin-up sequence for the Chaingun in order to make it a proper panic fast firing weapon.
*The full stop sequence lasts now 0.4 second if the weapon doesn't fire again during the spin-down sequence.
*Damage has been boosted from 10 to 11 damage per bullet.
-Modifications for tot4:
*Added details
*Instead of 6 gold keys, there is 3 gold keys & 3 silver keys, where the way to get them is color coded much like in tot3, in order to make navigation better. Due to this the way to find a specific secret has been slightly altered.
*Removed a turbine in the second coolant pool of level 3 to better distinguish the entrance and exit of the section taken from level 2.
*Finale has been revised.
*Fixed a softlock at level 3's final key's room.
*Fixed a softlock related to a specific secret
-Fixed a faulty shortcut on tot2
-Added silver key signs in the second temple room in tot5 to make the silver key door placement more obvious
-Added different health for each difficulty for the final boss' final phase.
-Disciple under supermonsters won't shoot in volleys anymore, instead his projectile will shock at faster intervals.
-Fixed a bug where the Fiend under supermonsters wasn't transparent.

Download link is the same.
Tomb of Thunder 1.02a

-Fixed a leak in tot1
-Fixed second goldkey lights in tot4's level 2 not triggering properly
-Fixed tot4's alternate entrances still displaying their names as "entrance A"
-Fixed a gold key room encounter in tot7 where one extra monster for hard skill didn't target the count to unlock the exit door
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This update mostly centers around map modifications:

-Made the Nail Infantry's bullet deal stronger damage (from 3 to 5)
-Made the axe kill on Nightmare harvest killed enemies' health divided by 5 instead of 4.5

-Map fixes:
-tot1:
* Made path to nailgun more obvious
* Made key doors more obvious
* Changed some monster placements (mostly for hard skill)
* Added additional teleporting monsters exclusively for when the quad damage is found

-tot2:
* Changed nailgun placement to first elevator shortcut
* Changed some monster placements (mostly for hard skill)
* Made usable computers more obvious
* Fixed an ambush where peeking through a gap in a wall would allow the player to see the upcoming monsters
* Fixed a fiend and ogre sharing the same space on normal skill (said ogre has been changed to a gladiator)
* Added a death knight and a fiend on normal to south-east region on normal skill
* Revised computer room in south-east region
* Made grenade launcher placement more obvious

-tot3:
* Made each colored key region's doors have lights of their respective colored keys to make them more obvious
* Changed some monster placements (mostly for hard skill)
* Made Invulnerability secret accessible from both sides of its location

-tot4:
* Fixed an issue on entrance B where the chaingun ambush would trigger too early
* Fixed an issue where both an ogre and vore would teleport at the same time
* Changed some monster placements (mostly for hard skill)
* Added white stripes to main stair shaft
* Fixed gold key signs & traps not triggering properly

-tot5:
* Made the silver key more obvious while also telling the way to go
* Gathering all gold keys now tells the way to go
* Changed some monster placements (mostly for hard skill)
* Changed last secret to an armor one
* Made the switch at the top of the light world's water tower more obvious
* Added specific colored pillars to indicate the placement of the tombs

-tot7:
* Gold Key Gate is now much more obvious
* Gathering all gold keys triggers a message to come back to the main tower gate
* Added green pillars pointing the way to the gold key rooms

Download link is the same.
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On top of the previous v1.01 fix:
-Fixed source files not matching what's inside the compiled progs files.
-Fixed duplicate zip file.
-Fixed series of shootable buttons leading to a secret in start.bsp where they were shootable multiple times, nullifying the challenge of finding the secret.
-Fixed possible softlock at the end of tot1.bsp, train doors now open permanently on top of their activator being locked behind counters.
-Railgun now does 95 damage on Deathmatch rather than the whopping 270 in Singleplayer for balancing reasons.

v1.011 fix:
-Added navigation aids for map 3, 4, and 5
-Fixed issues on map 3 and 5 on easy skill where counter-based critical encounters didn't trigger properly, making progress impossible
-Diminished fog amount for the final boss' third phase, making far-away targets easier to see

Download link is the same as before (mediafire link).