You will run the ".cc" file in NS-3 and it will generate the ".xml" file that you will open with animator.
The ".cc" should be a scenario that simulates a network running AODV or any other protocol.
For example you can use the /src/aodv/examples/aodv.cc which simulates AODV. However, you need to add the parts that will generate the animator xml file as explained in the previous reply.
Please read the tutorial to understand how NS3 works.