In order to unlock the secret ladder you are required to perform the following set of actions in this particular order:
1) Repair the upper deck gun
2) Repair the mid-deck left wing gun
3) Repair the lower deck left wing gun
4) Repair the hull
5) Repair the left wing engine
6) Repair the main engine
7) Repair the right wing engine
8) Repair the balloon
9) Repair the lower deck right wing gun
10) Repair the upper deck right wing gun
11) At this point a secret ladder should be activated.
12) Approach the chimney of mobula and perform a forward jump at it, attempting to grab an invisible ladder.
13) Climb all your way up to find a stowaway aboard your ship

Those systems are not required to be damaged, all you need is game registering the hits done in proper order.
Repairing the upper deck gun and main engine require knowledge of mobula parkour, if you are not familiar with those - please refer to a video guide below.