Release the Phantoms
If you choose to release the Phantoms, you’re siding with Anasko and his plan to wage war on the Settled Systems. You now have to reach the Pinnacle of the Scaled Citadel, which requires you to go through several levels of Phantoms and Zealots, who have infiltrated the facility. This is no easy task, as the route to get to the Pinnacle is long and will take you roughly five to ten minutes. There are also several routes to the upper levels blocked off by the blue glowing energy substance, making the journey even more difficult.
Eventually, after you reach the Pinnacle, you can find Anasko standing in front of a huge energy device. Here, Anasko tells you that your job is complete, but you won’t live to see the end of the plan. Essentially, Anasko is telling you you have to die. When he says this, you can either attack him or submit and die. If you choose to submit, the game restarts from when you entered the room. You’re not allowed to submit, meaning you can only attack.
By attacking Anasko, you now have to repeatedly deplete his health, as he can’t die yet, and shut down his machine. Shutting down the machine requires you to shoot and destroy four Modulators that can only be opened one at a time by activating specific switches around the room. Once you activate a new switch, look for where the Modulator is opening up and shoot it as quickly as possible. The Modulators are normally right near the switch, but the last one is outside of the room where the switch is located.
When all the Modulators are destroyed, you can leave the Scaled Citadel.