The Pulse of the Awakening is the signal initiating the end of the Proxy Project with the subsequent destruction of the remaining proxies. It is audible only to proxies. The Pulse activates involuntary genetic changes in the Amrita cells of proxies, making exposure to sunlight lethal for them.
Proxies were an essential part of the Proxy Project. As such, their task was to preserve the remaining human population on the planet with the creation of Dome Cities artificially populated through AutoReivs and WombSys. Proxies may have also functioned as living gene banks that can repopulate human and AutoReiv individuals as needed (which is why they are required for the WombSys to function).
However, the Proxy Project itself (including the Cogito Virus) was merely a contingency plan, and the main effort for the survival of the species was in reality, Project Boomerang. This involved the planetary evacuation ship, the Boomerang Star, which allowed a part of the human species to leave Earth.
When the conditions on Earth stabilize, the Boomerang Star would return and repopulate the planet. In that eventuality, Proxies would become unnecessary at best, and at worst, a hindrance.
To ensure that the Proxies do not interfere with the recolonization efforts, they were genetically programmed to self-destruct by involuntarily rendering their Amrita cells vulnerable to sunlight. Disintegrating them upon exposure. The signal for them to initiate this is beamed by the ship and is known as the "Pulse of the Awakening".
Proxies are designed to be unable to override this command. This drove most proxies in the series to despair and insanity at their impending deaths, as well as the loss of their reason for existence (their raison d'être).
Proxy One in particular, viewed it as a betrayal. He vowed vengeance by plotting to destroy the remnants of humanity that he was originally tasked to protect.
- That is when everything became perfectly clear. Everything about the malice implanted by the creator. We can not resist that which is. We simply... we simply have to punish them. Can you hear the pulse of the awakening?
Other proxies either destroyed their own human populations (like Kazkis Proxy and Senex Proxy), descended fully into madness (like Will B. Good), or willingly destroyed themselves (like MCQ). Both Monad Proxy, in her form as "Real" Mayer, and Proxy One were disintegrated by the sun.
Ergo Proxy (Vincent Law), however, was an exception. At the end of the series, by overcoming his despair, he voluntarily reverts these genetic changes, making sunlight harmless for him as it is on base humans.
The pulse is rhythmic in nature and is metaphorically depicted as the sound of a beating heart. In Episode 8, the chant of the madwoman of Charos (who might also be a proxy) refers to the Pulse of the Awakening growing stronger as the Boomerang Star (the "master") approaches Earth in space:
- Bit by bit it can be seen, bit by bit it can be heard. Bit by bit it grows stronger. Here, there, everywhere. The last beat, the master comes, riding across the moonlight that haunts the shadows in the dark places. He takes his time... I hear the pulse of the awakening along the moonlight that haunts the darkness. It will with certainly provide the time. The pulse of the awakening. The last beat. The master rides across the moonlight.
In the same episode, Senex also refers to the Pulse as a throbbing sound:
- The drums of war are beating. It is the music that brings the birth of a new world.