Is there a canonical source stating the fate of The Merovingian and/or The Twins (yes yes, there are other henchmen, but that straight razor guys are the coolest) during and after Agent Smith's "New World Order" attempt?
Answer
During the events that transpire while Smith had possessed the entire population of the Matrix, save for Neo, the Merovingian as well as any of the Exile programs would have been possessed. However the fate of "Merph" as well as other Exiles, the returned Agents, and those that survived the end of Revolutions is covered in The Matrix Online. The story lines from the game have been confirmed as the canonical continuation of the Matrix saga. As for the Merovingian he survives the reload of the Matrix, and is one of the three factions the player can choose to join in game. He primarily protected the Exiles, and was not necessarily in the middle of the hostilities between the Machines and Zion. One of the missions of his faction is to find the fragemts of the RSI codes for the Twins, once they are fully collected, the Twins are restored to full form and return to service to the Merovingian.

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