Here is the full list of all 16 Physical Layer achievements.
Start the game
Clear all missions of "Base242"
Clear all "DesertStone" missions
Clear all missions of "NEOCITY"
Clear all missions of "SNOWAREA"
Clear all "Zipangu" missions
Clear all missions of "Lastbase"
Clear all missions
Obtain the skin "Schoolniform"
Obtain the skin "SummerUniform"
Get the skin "AlterAgent"
Obtain the skin "Gymsuit"
Get the skin "Ninja"
Get the skin "MAIDCLOTHES"
Get all skins
Clear ONESHOT mode for all missions