The function of the One is now to return to the Source allowing a temporary dissemination of the code you carry reinserting the Prime Program. After which, you will be allowed to select from the Matrix, 23 individuals; 16 female, 7 male to rebuild Zion. Failure to comply with this process will result in a cataclysmic system crash killing everybody connected to Matrix which, coupled with the extermination of Zion, will ultimately result in the extinction of the entire human race.”
― The Architect.[src]
The Prime Program is the title which The Architect gave to the "Path of The One" (the process by which The One returns to the Source to allow the special code he is carrying to be disseminated in order for stabilizing the Matrix). In reference to computer programming, a prime program is a subprogram within a larger program (referred to as a proper program). In this case, the Matrix is the proper program, while the Path of the One is a subprogram within the Matrix.
A prime program is a subroutine that has a single entry point and a single exit point, with any number of decision nodes along the way. This subprogram was created in order to guide the One to the Source, which is the exit point for the Path of the One. This was confirmed by The Oracle, who stated that the Path of the One ends at the Source. Because reaching the Source is the exit point for the prime program, the One must reinsert it into the programming of the Matrix in order to start the cycle over again.
Upon reinserting the Path of the One into the Matrix, the entry point (the first decision which the One must make) is to choose 23 individuals to rebuild Zion. Eventually the One will die, the Oracle prophesies his return to the inhabitants of Zion, and many years later the next One arises in order to complete the Path of the One and repeat the cycle.
The Path of the One is a necessary subprogram to ensure that the One will act according to the Architect's wishes. It is one of the control measures created with the help of the Oracle, who understands the human psyche. The Path of the One is designed to create within the One a messiah complex. The One is granted special powers by virtue of his connection to the Source in order to make his role as a messiah believable.
Each decision node along the Path of the One is designed to create a sense of attachment between the One and humanity. Believing himself to be the savior of mankind, the One will take the necessary steps to ensure that humanity continues, albeit in an enslaved state. This process was subverted in the case of Neo, whose attachment to Trinity was stronger than his attachment to humanity. This love for Trinity was strong enough that he was willing to sacrifice humanity in order to save her.
The Path of the One is vital because 1% of the population inherently rejects living in the Matrix. In order for the Matrix to remain "balanced" and to continue to operate, the Matrix needs to be freely accepted by all of the humans hardwired to it. The Architect's own attempts to design the perfect Matrix, however, resulted in 100% rejection. And even though The Oracle's current version of the Matrix yielded nearly 99% acceptance, 1% of humanity still subconsciously rejected the system.
Each rejection (referred to as an anomaly by the Architect) is expressed in the form of a code within the Matrix which acts somewhat like a software bug. Over time, the number of rejections begin to build up and, after a certain threshold, this "systemic anomaly" must be purged from the Matrix or else the Matrix will eventually crash - killing everyone hardwired to it.
The solution is to take the remaining systemic anomaly, attach it to The One, and have The One bring it to the Source where it can be disseminated and destroyed. For this reason, The One is also referred to as the "integral anomaly", a proxy for all those who have rejected the Matrix.
By entering the Architect's chamber and choosing to return to the Source, The One essentially brings back balance to the Matrix, allowing for the system to reset. The balance, however, is only temporary, as it is only a matter of time before the systemic anomalies begin to surface, requiring the Prime Program to be initiated once again in a repeated cycle.
Reloading the Matrix is a separate step from reinserting the prime program. They can be confused as being identical because they occur at the same time. However, in the online video game The Matrix Online, it was confirmed that after the events of The Matrix Revolutions the prime program was not reinserted, even though the Matrix was reloaded. This simply means that the Path of the One no longer exists within the programming of the Matrix.
Neo, unlike the previous Ones before him, did not complete the Path of the One. Instead of going through the door on his right in the Architect's chamber, he left the Path of the One and went through the door to his left. This means that he left the Path of the One and began to follow the Path of Neo. Ironically, his own path still led him to becoming connected to the Source where he followed the original directive of the Path of the One.
Neo's unique contribution to the problem of choice was to make a deal with the Deus Ex Machina that the programming of the Matrix would now accept rejections. Those who desired to be free would be allowed to leave. This meant that when someone rejected the Matrix, it was no longer an anomaly. Therefore, with no anomalies threatening the programming of the Matrix, it was no longer necessary to have a One, which meant that the Path of the One was also no longer necessary. That is why the prime program was not reinserted. Because of the compromise made between human and machine, a state of peace was created.
The Prime Program as a Process
The “Prime Program” can also be defined as the process used by the Machines to stabilize the Matrix and reboot it every 100 years. It consists on a set of rules to be carried out to achieve those goals. It initiates when the Matrix begins to suffer a high amount of destabilization because of the 1% anomaly within it (“anomalies” being the humans that reject the program).
This Process works as follows:
When the instability has grown dangerously enough, the Machines randomly select a human to give him a Special Code that ties together that 1% anomaly of the Matrix to the human carrying said code. Thus, this human is considered an “Integral Anomaly”, he/she is, in essence, the SUM of all the anomalies within the Matrix. The role of this human (known as “The One” to those liberated humans believing the Prophecy) is to reach “The Source” (The Machine Mainframe) carrying this Integral anomaly to begin its dissemination, thus eliminating this 1% rejection. After this, the Matrix must be rebooted to stabilize it, (and along with it, reinstall the Prime Program, that is, the process described above, to assure that the next 1% rejection can be controlled and disseminated when the time comes) therefore giving it another 100 years of stability.
In order for this human to reach the Source, give his code and receive the help of the liberated humans to achieve both goals (although these goals aren’t known neither by these humans nor by The One, as they instead think they will end the war and save Zion), certain control measures are executed: the concept of “The Prophecy” is invented, claiming that a Special being (a Messiah/a Chosen One) will destroy the Matrix and liberate the human race from its Matrix enslavement along with ending the war against the Machines and thus saving Zion from its destruction. And to make this claim believable, this random human is not only granted with the code carrying the Integral Anomaly but also with a connection to the Source, which gives him/her a vast array of special abilities, that no other has. Special programs are also created to help him in his journey to the Source, the “Keymaker” being one of them, that helps him enter the door to The Architect Chamber each time the Matrix must be rebooted. The Oracle itself guides The One towards the Source making him believe he will save humanity. Another feature or control system of the Prime Program consists in giving special emphasis to “The One” feeling and becoming attached to humanity during his journey/path, in order for him/her truly believe he/she is The One and being fond of humanity, therefore not wishing to let Humanity die, thus choosing to go to the Source and stabilize the Matrix (and therefore doing what the machines want him/her to do), which stabilizes and continues the enslavement of humanity, but saves them from the Cataclysmic crash that would kill all humans. According to the Architect, this "attachment to humanity" feature of "The One" is purposefully designed and implemented, implying that along (or within) the code "The One" carries, it also carries this programming that makes him/her feeling attached to humanity.