What is the [Protocol]?
The Protocol is a widespread topic among higher beings aka the [Transcendent], this is largely due to its relationship with the [Architects], (the living-dead mechanical empire) and what exactly it entails.
The [Architects] and [Corruption] have a millennia long history of conflict with constant warring, at some point the [Architects] had repurposed their civilizations greatest creation the [Aeon Network] into a defensive weapon against the [Corruption] giving the network the so called [Protocol] for use in emergency. It is referred to as [Protocol Ouroboros] by the [Architects] and was designed as a defense mechanism against their long time enemy the [Corruption] if a cataclysmic event were to occur in their absence.
The Architects simply refer to the lower realms/multiverse as the [Pre-Protocol] world. The lower realm is where all transcendent originate before becoming immortals and entering the [Aberrant Realms]. A large percentage of the [Lower Realms] [95]% is suspected to be under control of the [Architects] and their [Aeon Network]. Occasionally there exist lower realms capable of exiting the [Lower Realms] and becoming an [Aberrant Realm], usually due to a large number of powerful individuals, this change usually requires a transition that occurs over a few hundred thousand years.
The protocol requires that a certain percentage of the [Aeon Network] & [Lower Realms] be corrupted before allowing use. [Protocol Ouroboros] is essentially a reset button for the lower realms/multiverse, specifically made so that the corruption can't devour and take control of these worlds, it is unknown if the protocol is actually capable of completely deleting existing corruption, however at the very least it is implied to be a sort of exterminator program.
It has four goals, the first is the most important, all lower realms are to be fragmented and reintegrated into a single world, this world is referred to by the [Architects] as the [Post-Protocol] world.
This world works by having so called [Aberration Barriers] essentially all the previously separate worlds are separated by a barrier regulated by the [Aeon Network], they work by altering the perception of individuals, it is suspected the [Architects] were unconfident in them when in regards to irregulars that are too strong to contain (Naruto, Otsutsuki, Acnologia, Ichigo, Soul King, etc.) it's believed this is why they made a deal with the [Players] & the [Celestial Abyss]. Most higher beings dispute the previous fact however, many believe that [Players] & the [Celestial Abyss] do not actually exist. However, should this deal exist, then these so called [Players] are implied to keep the irregulars in check to maintain equilibrium. This was the second function of [Protocol Ouroboros], the exact nature of its workings is unknown and often all information is redacted, though mentions of [Players] and [Protagonists] have occasionally been discovered.
The third function of the protocol is the activation of experimental bio-organic entities created shortly before their disappearance; they hold extreme similarities to the widespread race of humanity. They are meant to maintain the [Post-Protocol] world's order, acting as wardens for dangerous individuals, they also act as cleaners, working to find pockets of corruption missed by the protocol itself.
Finally there is the fourth and final function, the removal of both [Fate] and [Destinies] (Who are both tangible entities) influence over previously mentioned [Protagonists], it is suspected that this function was specifically implemented due to some favor or deal with the [Oracle] however these theories are largely unconfirmed.