Keep initiating DFM as soon as possible on Marko during the following five sequences:

1.At the start of the battle. 
2.A run over the Pentagon. 
3.When he blows up your allies on two bridges. 
4.When chasing him up past the Capitol building. 
5.When he begins his run on the White House and you can see the Washington Monument in the distance.
  Note: This is where you can actually shoot him down. 

You must initiate DFM as soon as possible because there is a secret timer, and when it expires, it 
will allow him to fire Trinity once. If you initiate DFM outside those five sequences, he will 
quickly perform a counter-maneuver on you.