Just an asterisks for this one, in case someone runs into this situation:
You'll likely end up with every quest in the game, done.
However, the trophy will still not unlock.
In most cases, Intelligence Gathering (5) is the quest you'll be missing.
The requirements are as follows, from a random post I discovered:
Phase 10: Oni Pursuit - War
Chapter 7: Age of Demon
Phase 10: The True King Awaken and The Age of Demon
Once you complete these, if the quest still doesn't pop, simply exit Online Mode or exit / re-enter the Command Center. This quest didn't appear until I left Online Mode and had gone to Yu in Story Mode.
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In my situation, I had every quest in the game done except for Intelligence Gathering. I have 100% of all Story Missions done.
I also had 100% of Phase 1 - 9 done.
I have 5-10 missions in every other phase done.
The only one I didn't do in Phase 10 (I was working towards it) is Oni Pursuit - War.
As soon as I had completed Oni Pursuit - War, the quest became available.
There are a couple of sources that have said that the requirements above wasn't enough in some cases.
If anything, if you're going for Platinum, simply go the course and complete every mission like you're supposed to, this quest will eventually pop.
As it stands, as far as I can confirm from my own experience
All Story Missions at 100%
Phase 1 - 9 at 100%
All Red Missions in Online Mode.
Oni Pursuit - War
A few missions here and there in all other phases (one of these may have been a requirement) caused this quest to pop.