Ryuuki Heidan Danzarb(1993)

Danzarb is a quirky sci-fi mecha RPG. It´s segmented into chapters or episodes, each having a minigame or puzzle for you to solve. In one, for example, you´re tasked with locating a bunch of ID card segments then you have to do a little sliding puzzle to put them together. In another, you collect clues to a time bomb defuse sequence from enemy soldiers, and you have to piece them together in a logic puzzle to decode the sequence.