Where does the rod that opens door that is attached to door handle go it has come off inside door?

This is hard to explane this way but I will try ok. On the handle there is a plastic lock (see pic). This goes into the hole on the handle then the rod goes through it and then you push the clip over the rod to lock it.

Just to added to this one the other end is attached to your door latch you will see a clip similar to the one racefan posted where the rod is missing where it goes.

The best way to do it would be to remove the outter door skin that will give you a full view and access to the inside of the door.

Is it the passenger or drivers side door?

Alright the cover behind the drivers mirror pops loose and you will need a 2 or 2.5mm allen wrench to loosen the screw holding the mirror cover to the remote control for the mirror. Then remove the three 10mm nuts then remove the mirror. Then at the end of the outter belt molding you will find a torx T-15 screw remove it and pop the outter belt molding off. To remove the outter door handle there is a plastic pin that you have to slide the center of the pin towards you then the pin will come out. Then the door handle slides to the side and comes off. Now there are T-30 bolts all around the outter edge of the door panel remove them and then the outter door skin will come off.