Use the table of contents to navigate to whichever mission you're currently doing. The numbering order was 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 chests as well as the 'unidentified blueprint'. The icon's size is not indicative of what type of chest/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. (I realize this icon is pixellated in the mission maps)

Red Triangle -> villain that drops an encrypted dataslate
-The dataslates are used to unlock the cogitator in mission 4. Only one is required.

Red Box -> cogitator for unlocking covert missions

Red Diamond -> covert mission (this is a crusade map icon)

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

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=2224902710
The numbers below have been converted to my numbering.

"Mastery Path"
1 - 2 - 3 - 4 - C -
5 - 7 - 8 - 9 - D -
11 - 12 - 14 - 16 - B -
13 - 15 - 6 - A - 17 -
10 - 18 - X

Completing this mission unlocks Secret Mission A.

Completing this mission as well as Mission 16 unlocks Secret Mission B.

Must successfully aid the Stormwatcher to unlock the cogitator which unlocks Covert Mission D.

Completing this mission as well as Mission 7 unlocks Secret Mission B.

Unlocked via completion of Mission 3.

Unlocked via completion of 7 and 16.

There are only five info-fragments, https://steamhost.cn/steamcommunity_com/app/527430/discussions/1/1752394042379382949/

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


Credits:
https://steamhost.cn/steamcommunity_com/profiles/76561197960850097 for helping test loot spawns.
https://steamhost.cn/steamcommunity_com/profiles/76561198051945630 for helping test loot spawns, mission unlock conditions, and for catching a mistake with the mission 16 map.
https://steamhost.cn/steamcommunity_com/profiles/76561198092241169 for the 6/7/23 update

Patch notes:
12/24/2019 ->
-updated the crusade map, map key, and final notes
2/13/2020 ->
-cleaned the crusade map
-fixed maps for mission 9 and 16
-added notes for mission 9 and B
-updated the map key, overview, and added 'Credits' to the final notes
4/01/20 ->
-updated the guide overview and the "Note about the mission maps"
5/25/20 ->
-linked the amber guide
6/26/20 ->
-linked the viridian and azure guides
-noted which links go to which guides for ease of reference
9/5/20 ->
-updated a couple section titles and added notes under a few missions to make it easier to reference unlock conditions for certain missions
-linked the zircon guide
2/12/21 ->
-linked the Violet guide, linked a fellow guide-writer's void crusade path recommendations
8/18/22 ->
-linked the Crimson guide
6/7/23 ->
-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