Seems to be the hardest Protocol for most people to find including myself. The Chromatic Protocol is rewarded when defeating the Echo of Iska boss fight.

To find this boss fight simply teleport to the WAREHOUSE Obelisk in ARDEN, go up the stairs, across the bridge, directly through the next room, into the room where the red guy teleports in (green bubble), enter the door directly behind him, go all the way down the winding staircase and through the door. The nearest locked door across the small bridge will be the boss room. Try your best to defeat her the first time which shouldn't be difficult for end game players as there's been reported bugs of her disappearing when entering a second time.