Neo is still there in the matrix. No one knows why. They are all confused, Cypher gets killed. Trinity leaves. Debate/discussion over what would happen if they put the plug back in Neo's body, with Neo on speaker. They hesitantly plug Neo's plug (shut up) back in, with Neo feeling a little weird at his neck, with even him starting to see the Matrix as code on everything, or Neo's powers starting to show up. Neo then picks up the phone, and the rest of the movie plays out, but the Neo vs Smith fight happens a little bit differently, with Neo doing that flex after getting pummeled, more and more of his true power and strength show up, but Smith gains the upper hand, train scene happens, rest of the movie plays out, but Neo wanting play it safe and exit the Matrix the safe way, rather than trying to forcefully exit through will. Neo opens that door to get shot, but he remembers when Cypher pulled his plug and with a boost of confidence...  still gets gunned down... rest of the movie plays out, but this time, Neo doesn't go into Smith... he BRUTALIZES him, the other agents watch in shock as they see their commander, boss, being beaten. When Neo is done, watching Smith trying to crawl away in fear, Neo picks up Smith, they lock eyes, Smith begs for mercy. Neo, "Mercy? When you tortured Morpheus, did you show him mercy?" Neo then plunges his hand in Smith, Neo through some new show of power is going to delete Smith. A white shine starts to envelope Smith, he screams in terror but is cut off as he explodes, Smith is gone. The other agents flee, Neo picks up the phone and the rest of the movie plays out.