Its a program folks don't you get that part?

Neo is basically an antivirus program and Smith is the virus....in order to take out a virus you attack its core code, once the core code is gone the rest of the virus dies or dissapears.

You guys are reading way to hard into this its simpler than you think it is.

The Train is nothing more than an information pipeline and the Train master is the protocol the programs need in order to access any area of the Matrix.