To find the anomalies, you must be in the Aether. Until then, you will have completed each of the challenges listed above, with the optional challenge being obtaining the DIE Machine. Assuming you've done everything else, you'll likely find the Aether portal in the medical bay. So the Aetherscope essentially works in conjunction with another element - Dr. Vogel's journal. So your main challenge once you get the scope should be to go back to the Aether and then go to Medical Bay.
The Medical Bay is on two levels and on the upper level you will find a room with a computer. This is where you'll want to go with the Aetherscope to hang the newspaper.
Pick up Doctor Vogel's Journal in the Medical Bay
Journal in hand, you can quickly find anomalies and complete this Easter Egg leg which will essentially set up a containment trap when you make your way to the final boss. So after you get the log just head downstairs to Med Bay. Behind the speed perk machine, you will find an anomaly as you approach. Keep in mind that you cannot see these anomalies from a distance. The glowing orb will only become visible when you get close and you will need to interact with it first, THEN interact with it again to give Vogel's journal.
Anomaly and - Med Bay
Assuming you don't run out of meds once you grab the diary, this anomaly is pretty much right below you. Once you've triggered this first anomaly, a power zombie named Mayak will appear.
Anomaly 2 - Control room
Go up the stairs to the main hallway, then hang left to go to the control room. This is the room with the broken glass containers. It also contains reward and challenge machines. Approaching Med Bay, the anomaly will be on the right side.
Anomaly Three - Particle accelerator
Return to the Particle Accelerator room and return directly to the workbench on the ground floor. The last anomaly is here.
Once you've triggered all three anomalies and given the log, simply go back to the Med Bay computer (you need to exit the Aether) and use the computer with a password. This will open the containment device.
