1) the merovingian accepted trinity's terms and released neo instead of opting for a gunfight in which everyone, including himself, would probably die.
2) agent smith absorbed seraph and the little girl. that's why smith repeated to the oracle what she had told the little girl earlier. smith pretty much absorbed everyone in the matrix and made it into his own little world. once smith died, the architect basically rebooted the matrix (hence the black cat reference in regards to experiencing deja vu when something was changed in the matrix) and all of the programs were restored to normal.
2) agent smith absorbed seraph and the little girl. that's why smith repeated to the oracle what she had told the little girl earlier. smith pretty much absorbed everyone in the matrix and made it into his own little world. once smith died, the architect basically rebooted the matrix (hence the black cat reference in regards to experiencing deja vu when something was changed in the matrix) and all of the programs were restored to normal.
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