In the first mission, the location of the NSF Commander has been randomized into one of five locations. Without sequence breaking, it is necessary to find the commander before you can progress. Once you have talked to (or killed) the commander, all NSF troops on the island will die.

The commander can be placed behind the arcing electricity in the small open bunker

The commander can be found hiding in the small storage hut opposite the entrance to the statue. This area is usually heavily patrolled.

The commander can be found in the jail cell where Gunther is.

The commander can be found at the dock where Paul and Corporal Collins are. Very suspicious they didn't notice.

The commander can be found at the dock where Harley Filben is.

The commander can spawn on the upper level of the outside area of the statue base, near where there are two NSF troopers having a conversation (just inside). Note that the commander is easily spooked, so if you kill an enemy near him, or set off an explosion, he can start running and can end up stopping somewhere else in the outside area (Often on one of the ramps, which can be tricky to see)

The commander can also stay in his vanilla location at the top of the statue

The boat to leave is also in a randomized location.

The boat can be in its normal location at the dock.

The boat can be hovering at the top of the statue.

The boat can be at Harley Filben's dock.

The boat can be near the storage hut in front of the statue.