9/22/2017 Update Regarding WotC Compatibility: I've been told that the War of the Chosen expansion adds duplicate files to the game that may require additional steps than what this guide provides. I've yet to buy the expansion, thus I'm unable to provide adequate support for those attempting to adapt this to WotC. Please consider this guide for vanilla XCOM 2; WotC adaption may require some .ini file exploration of your own. =)

NOTE: The ini files refer to the different difficulties as Easy (Rookie), Normal (Veteran), Classic (Commander) and Impossible (Legend). Adjust which values you change accordingly.

Step 1: Locate and open the DefaultGameData.ini file in Notepad. For me this file was located in C:\Program Files (x86)\Steam\steamapps\common\XCOM 2\XComGame\Config ; your path might slightly differ.

Step 2: Press Ctrl+F within Notepad to bring up the search bar. Search for "FacilityDoomAdd". It should bring you to this block of text.

FacilityDoomAdd[0]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Easy
FacilityDoomAdd[1]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Normal
FacilityDoomAdd[2]=(DoomChances[0]=(DoomToAdd=1, PercentChance=75), DoomChances[1]=(DoomToAdd=2, PercentChance=25)) ;Classic
FacilityDoomAdd[3]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Impossible

For the difficulty you wish, set DoomToAdd=0 and PercentChance=0. For Classic (Commander) difficulty, you'll want to do this twice to both sets of value on it's line.

Step 3: Our next stop is the very next block of text.

FortressDoomAdd[0]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Easy
FortressDoomAdd[1]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Normal
FortressDoomAdd[2]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Classic
FortressDoomAdd[3]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Impossible

Here, we're changing DoomToAdd=0 and PercentChance=0 just like in the last step.

Step 4: Search for FacilityStartingDoom. It should bring you to these two blocks of text.

FacilityStartingDoom[0]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Easy
FacilityStartingDoom[1]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Normal
FacilityStartingDoom[2]=(DoomChances[0]=(DoomToAdd=1, PercentChance=75), DoomChances[1]=(DoomToAdd=2, PercentChance=25)) ;Commander
FacilityStartingDoom[3]=(DoomChances[0]=(DoomToAdd=1, PercentChance=100)) ;Impossible

FortressStartingDoom[0]=(DoomChances[0]=(DoomToAdd=3, PercentChance=100)) ;Easy
FortressStartingDoom[1]=(DoomChances[0]=(DoomToAdd=3, PercentChance=100)) ;Normal
FortressStartingDoom[2]=(DoomChances[0]=(DoomToAdd=3, PercentChance=100)) ;Commander
FortressStartingDoom[3]=(DoomChances[0]=(DoomToAdd=3, PercentChance=100)) ;Impossible

Repeat here what you did for the previous two steps.

Step 5 (Optional): Search for MinorBreakthroughDoom, and it will bring you to this:

MinorBreakthroughDoom[0]=1 ;Easy
MinorBreakthroughDoom[1]=1 ;Normal
MinorBreakthroughDoom[2]=1 ;Classic
MinorBreakthroughDoom[3]=1 ;Impossible

MajorBreakthroughDoom[0]=2 ;Easy
MajorBreakthroughDoom[1]=2 ;Normal
MajorBreakthroughDoom[2]=2 ;Classic
MajorBreakthroughDoom[3]=2 ;Impossible

These affect the amount of progress the Dark Events associated with Avatar Project provide if completed. Set the =1 or =2 to =0 if desired.

Step 6: Save the file. You're done!

A Final Note: I applied these changes mid-campaign, and initially it's didn't appear to work. It seems to me like the game will queue up project progress a bit in advance and you're likely to get another block or two before your changes kick in. That said, stick with it because this does work.

Have fun, Commanders!