Operation Babel: New Tokyo Legacy

Story related and cannot be missed.

Unlocks upon completing the mission "7H, GHQ Cemetery"

Head to Aoyama Road then GHQ Cemetery - Main Gate. To advance, you need to trigger some switches. To proceed to the West Catacombs, trigger the switch at X17 Y08 West and the switch at X06 Y16 West. You will fall through. Go through the short passageway and you'll reach a party of the cemetery that was previously inaccessible. There is another staircase to go down, and you will be told to abandon the mission. Choose to ignore the "warning" and continue.

You have to head to the Satan area. When you reach the bell, ignore Kaito's and Noriko's suggestions and ring the bell twice. This opens up a portal in Catacombs - Central at X10 Y10. Head to the portal.

Select "Refuse" and then select "Yes", and then "Defy". You will fight Joker. Attacks can cause confusion. He can also shuffle your party. He likes to hide behind reinforcements, so range attacks are useful. He can use a spell that makes him immune to ranged attacks, but it can be nullified with the Academic's Default Target spell.