does anyone know how neo will destroy the matrix

no, seriously, i don't know.

I think Agent Smith will infect the entire Matrix by copying himself to everyone and infecting every program.

There may be some disagreement on this; but because Agent Smith is unplugged so will everyone he infects.

We can only assume that a person taken over by Agent Smith isn't experiencing their Matrix fantasy anymore and if they make up from the Agent Smith Infection; then the would be out of the Matrix all together.

Therefore the problem is how do you disinfect someone unplugged by the Agent Smith Self Replicating Virus:

Answer: Anti-Virus Software like the kind that was guarding the Oracle.

Now that everyone is free from the Matrix it has been effectively destroyed; but that still leaves the problem of dealing with the physical machines... perhaps a massive EMP blast.

Neo is a cyborg, it isnt Neos Agenda to destroy the Matrix, see 4th Movie thread for more info

do you have any prof that neo is a cyborg, i dont think he is, there is more proof if any that he isn't a cyborg than that he is.;)