At 26:25 (Minutes) - 26:34 (Minutes) Nikita loses her gun getting on the motorcycle to chase the suspect getting away in the truck. At 27:52 (Minutes) she reaches back and uses the same gun she lost getting on the motorcycle.
After realizing that the rocket did not kill Michael, Amanda could have ordered Sonya to fire the three remaining Hellfire missiles from the Predator drone to kill Nikita and Michael.