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 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 -> 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 covert or secret missions

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

Purple Oval -> teleporter
-Only teleporters that go to rooms with other map-key objects are marked.

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://steamproxy.net/sharedfiles/filedetails/?id=2181562638
The numbers below have been converted to my numbering. Brackets indicate optional missions (i.e. if you've got extra time).

"Path through the Void Crusade"
3 - 2 - 1 - 5 - 6 -
7 - 4 - 10 - 13 - 14 -
8 - 11 - 16 - 18 - 21 -
20 - B - 19 - 17 - 12 -
A - 22 - 15 - 9 - X

"Tarot Farming"
3 - 4 - 9 - 16 - 13 - 17 - Y

"Info Fragments path"
1 - 3 - 4 - 2 - 5 -
20 - 21 - 9 - 16 - 17 -
[7] - - Z

Must successfully aid the Stormwatcher to unlock the cogitator which unlocks Secret Mission 11.

Cogitator unlocks Secret Mission 19.

Dataslate allows you to access the cogitator in mission 13.

Unlocked via the cogitator in mission 4.
The cogitator here unlocks Covert Mission A.

Must acquire the encrypted dataslate from Mission 10 to access the cogitator in this mission which unlocks Secret Mission 14.

Unlocked via the cogitator in mission 13.

Unlocked via the cogitator in mission 5.

\

Completing this mission, as well as mission 21, unlocks Covert Mission B.

Completing this mission, as well as mission 20, unlocks Covert Mission B.

Unlocked via the cogitator in Secret Mission 11

Unlocked by completing missions 20 and 21.

Nothing here.

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

Credits:
https://steamproxy.net/profiles/76561198092241169 for the 6/7/23 update

Patch notes:
5/03/20 ->
-fixed the note under Mission 4
5/25/20 ->
-ivory guide has been updated so the note about it being outdated has been removed
6/26/20 ->
-linked the viridian and azure guides
-noted which links go to which guides for ease of reference
10/14/20 ->
-added notes under certain missions and updated the titles of certain missions to make unlock conditions easier to reference
-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 paths
-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