The 2nd mission is once again fairly simple. You’ll be given 4 Commandos and a Chinook. Take them to the flare in the south to recover the base. There are a number of areas here cut off from each other by a river. Take a Commando in the Chinook to carefully explore each section. Once you find a dinosaur use the 2 choppers to take it down.
With all the dinosaurs taken care of you’ll proceed to the next mission.