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 Box -> cogitator for unlocking secret and covert 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 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://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=2224889822
The numbers below have been converted to my numbering.

"Mastery Path"
2 - 6 - 4 - 5 - 1 -
7 - 8 - 10 - 11 - 9 -
A - C - 17 - E - 12 -
D - 18 - B - 13 - 19 -
3 - 16 - 15 - 14 - X

Completing this mission and mission 11 unlocks Secret Mission B.

Cogitator unlocks Secret Mission A.

Cogitator unlocks Secret Mission C.

Completing this mission and mission 2 unlocks Secret Mission B.

Must successfully aid the Stormwatcher to access the cogitator.
Accessing the cogitator in this mission, as well as completing Secret Mission C, unlocks Covert Mission E.

Unlocked via the cogitator in Mission 8.
Must successfully aid the Stormwatcher to access the cogitator here which unlocks Covert Mission D.

Unlocked via completion of Mission 11 and Mission 2.

Unlocked via the cogitator in Mission 9.
Completing this mission, as well as accessing the cogitator in Mission 17, unlocks Covert Mission E.

Unlocked via the cogitator in Secret Mission A.

Unlocked via both accessing the cogitator in Mission 17 and completing Secret Mission C.

Nothing here.

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

Credits:
https://psteamcommunity.yuanyoumao.com/id/Wolfilein/ for a donation of shards.
https://psteamcommunity.yuanyoumao.com/profiles/76561198020159309 for an assist with mission unlock testing.
https://psteamcommunity.yuanyoumao.com/profiles/76561198092241169 for the 6/7/23 update

Patch Notes:
3/25/22 ->
-fixed the section title for the final section
8/18/22 ->
-linked the Crimson guide
-added a credit
-fixed Secret Mission B's unlock condition
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