Use the table of contents to navigate to whichever mission you're currently doing. The numbering order was roughly determined by the order in which I ran the missions when I made the screenshot of the crusade map.

Yellow box -> chest or loot
-This icon covers all types of static loot like chests and unidentified items. The icon's size is not indicative of what type of loot is there.

Blue 'Diamond' -> info-fragment
-For revealing the contents of end-crusade loot chests. Omicron Arkh has a voice line that lets you know when one is nearby.

Red Triangle -> enemy that drops an encrypted dataslate
-The dataslate is used to unlock the cogitator that gives you access to a secret mission.

Red Box -> cogitator for unlocking secret missions

Green Star -> relevant secondary objective
-Only secondary objectives that unlock something upon successful completion are marked.

Note about the crusade map:
The small yellow number in each mission icon is the corresponding difficulty increase.

Note about the mission maps:
I've rotated them to at least approximately match how the map is oriented at the start of the mission.

https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2224866298
The numbers below have been converted to my numbering.

"Mastery Path"
1 - 2 - 3 - 4 - 5 -
21 - 20 - 24 - 6 - 8 -
10 - 9 - 12 - 14 - 16 -
17 - 15 - 19 - 11 - 13 -
23 - 22 - 18 - 7 - X

Must successfully aid the Stormwatcher to access the cogitator which unlocks Secret Mission 9.

Unlocked via the cogitator in Mission 6.

Completing this mission unlocks Secret Mission 22.

Dataslate allows you to access the cogitator in Mission 14.

Completing this mission unlocks Secret Mission 23.

Must acquire the encrypted dataslate from Mission 12 to access the cogitator in this mission which unlocks Secret Mission 16.

Unlocked via the cogitator in Mission 14.

Completing this mission unlocks Secret Mission 24.

Unlocked via completion of Mission 11.

Unlocked via completion of Mission 13.

Unlocked via completion of Mission 20.

Let me know if I missed anything or if there are any typos/formatting issues.

Credits:
A nice fellow who donated the shards I needed. Asked not to receive a credit so this will remain anonymous.
https://steamhost.cn/steamcommunity_com/profiles/76561198092241169 for the 6/8/23 update

Patch Notes:
8/15/20 ->
-reuploaded the crusade map, steam broke the original upload
2/12/21 ->
-linked the Violet guide, linked a fellow guide-writer's void crusade path recommendations
8/18/22 ->
-linked the Crimson guide
6/8/23 ->
-added a section for Grimstalker's recommended path
-changed the link to Grimstalker's stuff from the general link to the link for the specific crusade and moved it to the dedicated section from the basic guide info section