Story related and cannot be missed.
Once you defeat the boss of level 3 the achievement unlocks during the cut scene that follows. To defeat the boss, first pound on him a bit and he will fly away to the front corner. Run to the back and flip the switch to raise 2 boxes. Switch to Humungosaur and pull the left box to the left slot. Another switch will rise beside it so go ahead and press it to have the crane pick up the box and damage the boss. Now take the right box to the right slot. Be sure to block the boss's attacks as needed, especially his red laser attack. Anyway, another switch rises so press it for some more damage. This will open the hole in the middle so switch to Armodrillo and drill the hole until the middle platform is below the laser field. The boss will now be forced to come back to you so just pound on him until he is toast. You can use the crates to get life back during the fight if you need to.