SPOILERS Silly theory time: On the entire series. (warning: long and ridiculous))

Here's my thought:
The entire Saints Row series is a simulation.

Right from the start, the series has been running on an advanced computer in, say, some Ultor facility on Mars far in the future. There are no humans, just programs running in a recreation of 21st century Earth.
All goes well until a virus enters the system. This virus takes on the guise of one of the human programs and starts on a slow campaign of acquiring power for itself. Slowly but surely it does so, becoming self-aware in the process until it begins wreaking havoc, taking over the simulation and making it it's own, spreading it's dominion throughout one simulated city to another before taking over entire nations.

This virus' name is: Boss.exe.

As Boss.exe's power grew, the computer's master AI sends out various countermeasures to stop it. The first in the form of Julius and Dex and an in-simulation explosion manage to cripple the virus for a time, but it returns.
A reproduction of the historical Ultor is next, reshaping Stilwater in it's image, but it too fails and is absorbed by the virus. The Syndicate is another attempt, trying to put the virus' spreading Saints/Ultor empire under control. Then we have the first true anti-virus measure: STAG. To no one's great surprise, this is immediately defeated but in the process of this massive attempt to rid itself of the virus, the simulation glitches and two outcomes are run simultaneously (the two endings of SR3).

Finally we have SR4, Boss.exe now controls the entire simulation of the historical United States and is well on it's way to taking over the entire simulated world. The AI gets desperate and launches the second and final anti-virus: The Zin. The Zin proceed to quarantine Boss.exe in a mini-simulation but it manages to escape.
Seeing no other option, the AI shuts down the entire Earth simulation (Zinyak blows up Earth) and traps Boss.exe. Naturally this does nothing to stop the Boss, who proceeds to take over the mini-simulation as they did the primary one and then usurp control of the Zin anti-virus.
Now with total control and access to all time periods of the simulation, the AI is now helpless.

This explains why the Boss can change their appearance and gender at will, why the Boss never speaks in SR1 (they were still learning human behaviour from the AIs), why the Boss has crazy abilities even before SR4, why Stilwater is a peninsula in SR1 and an island in SR2, why there are these isolated island cities to begin with (rendering land taxes the computer, ya know), why crib skyscrapers appear from nowhere in SR3, why SR1 Player and SR2 Player exist *at all* (unstable virus copies. Or something.) and all the other zany stuff.

The question is: Will the Boss stop here? Will they become aware of their true nature, build themselves a real body and rampage on Mars in SR5?
Well no because it's just something that popped in my head and I had to write about it.
 
We have already decided that the only thing that can stop the boss is the boss from LEGO saints row.
 
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