When Smith pulls up in an Audi at the beginning of M2, his license plate is "IS 5416". In the King James Bible, Isaiah 54:16 reads:
Behold, I have created the smith that bloweth the coals in the fire, and that bringeth forth an instrument for his work; and I have created the waster to destroy.
As powerful as the virus Smith is, he still would have been powerless against the Trainman inside of Mobil Avenue, where the Trainman is "God". The Merovingian (a programmer) would have been able to disable Smith's virus code before Smith exited Mobil Avenue. Or, he would have been able to hold Smith in Mobil Avenue indefinitely. Either way, this is how the Merovingian is able to exert control over almost every exile program in the Matrix.
However, none of this really applies to Smith since he is a sentinel (or some kind of "super" sentinel since Agent Smith was an Arch-Agent). Sentinels have independent access to the Matrix. For more on agents and sentinels, see Matrix System: Agents.
It is important to note that "Agent Smith" was present during M1, but in M2 and M3, he is referred to only as "Smith" since he is no longer an Agent of the system. This section deals solely with Smith, not Agent Smith.
Smith: The New Smith
Smith: Mother Oracle
Smith: Smith's Defeat
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