Agent A: A puzzle in disguise

This achievement is story related and cannot be missed. It is unlocked at the end of the game when you successfully complete the mission and are climbing up the ladder. The preconditions are as follows:

Discover Ruby's submarine as outlined here: Solution for Super Sleuth In Agent A: A puzzle in disguise

Once you enter the doorway unlocking the above achievement, immediately grab the bolt cutters you see in front of you and exit. Take the boat to the lighthouse. Go to the top. Use the bolt cutters on the chained cabinet and take a wrench and a valve handle.

Return to the submarine and highlight the control panel. Use the wrench on it to open it. Attach the small valve handle and turn it until it overheats and blows. Exit the control panel. Ruby will enter and 'escape' in the submarine. Exit the cavern on the far side (not through the doorway you came in) to go to the beach. A cut scene will:
On the beach, investigate a mound to find Jerry Jetpack and press his red button. The ensuing cut scene
Following the cut scenes, a ladder will appear. Climb up it to unlock this achievement.