Watched Matrix Revolutions the other day. I think I figured it out. Neo lets Agent Smith take him over. Smith thinks he’s won. But it’s only through taking on Smith’s form that Neo is able to spread his essence to all the Smith duplicates and shatter them, leaving behind the people (and programs) they once were. Reminded me of I Cor. 15:22, “For as in Adam all die, so in Christ all will be made alive.”
Because, in the same way, Christ took on the sin of the world and died. Right then, the power of sin and death was broken and the veil was torn, allowing the Holy Spirit to spread throughout the Earth.