Operation Babel: New Tokyo Legacy

Sometime after completing a "A Call from Alice" (just go around getting into fights), when you return back to Headquarters, you'll get the mission "7H Repeat Elimination". After defeating all of the 7H again, you submit this mission. This opens up all of the Embryo Arcs. There are 7 Embryo Arcs, and they can either be accessed through random portals on certain maps (won't appear on the map screen), or via the Babyl Sphere. If you try to access via the Babyl Sphere, you'll have to fight the appropriate 7H again, but once they die, they won't be resurrected again, and besides, you'll need to defeat all 7H again to access Lethal Hall. Here is how to access each Embryo Arc and how to complete them:

I
Shinobazu Prison
Babyl Sphere - Shimna

The boss is located at X15 Y07. There are dispel zones located in depths in the southwest part of the map, but they are not necessary to pass through there. Those areas can only be safely passed with all current party members equipping items with the float ability. The boss is Golden Rock, and it's quite strong. The Clone Nono and Clone Yuyu can be contracted.

II
Green Museum
Babyl Sphere - Buccaneer

The boss is located at X10 Y18. This dungeon is nothing special. The boss is Leviathan with Killer Orca (2), Eelvern (5), Death Flipper (3). Easy fight.

III
GHQ Cemetary
Babyl Sphere - Wizer & Walpurgis

The boss is located at X10 Y11. You need to head to X08 Y07 and use Enfloat here because it's not in a dispel zone. The boss is Reuse Y Wizar & Reuse Pulsar.

IV
Haunted Hospital
Babyl Sphere - Joker

The boss is located at X01 Y15. You need to pull levers at X07 Y02 and X09 Y14. There are passable walls at X19 Y03, X07 Y08, X08 Y12, X07 Y15, X19 Y08, and X06 Y19. The bosses are Soul Eater, Soul Rebirth, and some Code Erasers. Soul Eater is weak to light and Soul Rebirth is weak to dark.

V
Geomatrix
Babyl Sphere - Dreadnaught

The boss is located at X09 Y10. This dungeon is mostly one way doors and dark areas, but other than that, it's nothing special. The boss is Replica Z Wizer with 3 Replica Feathers.

VI
Aoi Shine
Babyl Sphere - Thanatos

The boss is located at X02 Y04. This dungeon has a lot of doors. The boss consists of 2 Muramasa Rabbits, 3 Eraser Grids, and 4 Code Erasers, which are nothing special at this point of the game.

VII
Embryo
Babyl Sphere - Fuhrer

The boss is located at X01 Y16. There are a few locations where there are depths with dispel zones so be careful. Those areas can only be safely passed with all current party members equipping items with the float ability. There is a lever at X02 Y13, which is necessary to progress. The warp at X13 Y13 is the correct warp to progress. The boss is Clone Akashic.

Note: After completing any Arc, you get a cutscene when you return to headquarters and you unlock the assignment "Embryo Core Accident", which is required to unlock Lethal Hall.