In The Matrix Reloaded, the Oracle explains what happens to programs that are flagged for deletion:
Neo: Programs hacking programs. Why?
Oracle: They have their reasons, but usually a program chooses exile when it faces deletion.
Neo: And why would a program be deleted?
Oracle: Maybe it breaks down. Maybe a better program is created to replace it - happens all the time, and when it does, a program can either choose to hide here, or return to The Source.
According to the Oracle, programs are flagged for deletion "all the time". However, while I can think of many programs that chose to hide in the Matrix as Exiles, I can't think of any program that chose to return to The Source (i.e. voluntary deletion). Obviously, we are more likely to see Exiles rather than programs that chose deletion for two reasons:
- a program that chose deletion wouldn't be around for us to see whereas Exile programs often still exist and can be seen
- the Oracle says a program "usually" chooses exile.
Nonetheless, the fact that programs "usually" choose exile implies that some do not.
Do we know of any programs that voluntarily chose deletion instead of exile? We know some of the history of the Matrix and it's possible that a program figured prominently enough to be mentioned in that history yet also chose deletion after breaking down or becoming obsolete.
Note: The program does not necessarily need to be humanoid (e.g. Agent, vampire, etc.). The Oracle mentions that programs have been written to govern birds, trees, the wind, etc. An example of any program that voluntarily chose deletion is acceptable.
Answer
The very short answer to this one is "no".
There are a considerable number of programs and exiles seen in the Matrix Trilogy, but the overwhelming majority of programs we meet (Agents, for example) are doing precisely what they're supposed to be doing. Those that aren't are invariably exiles with their own agendas that aren't aligned to the Zionese rebels.
At no point do we see a program accept deletion although we do see a number of programs who've been superseded that don't return in the films such as Agent Brown and Agent Jones. It's certainly possible that they chose to return to the Source.
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