Contact (U)(Psyfer) ROM

The story begins with the Professor flying through space, fleeing from a mysterious enemy known only as the Klaxon Army (CosmoNOTs - "Cosmic Nihilist Organization for Terror" in the US and European releases). He ends up crash landing on a strange planet, losing the "cells" that power his ship. Without power, he is stranded. He enlists the help of Terry, a young boy. Terry agrees to help the Professor by exploring the planet and locating the cells. Helping the Professor is the only way that Terry will be able to get home, but the Klaxon Army are tracking them down, the cells are hidden in some dangerous areas and, as the game progresses, the Professor's intentions are slowly thrown deeper and deeper into question.
The player is included in the storyline as a separate character from Terry, and the game's characters recognize the player as "controlling" Terry using the DS, breaking the fourth wall. Throughout the game, the Professor will talk directly to the player to give hints on how to use the controls and to voice his concerns about Terry. The Professor is eager to keep the player's existence and their role in Terry's life a secret from the boy.

From the get-go, this game is insane. It IS made by Atlus after all, the same people responsible for the Shin Megami Tensei franchise, as well as the Persona franchise and a flurry of other games. The game begins right away with a scientist on a space ship breaking the fourth wall, and from there, things only begin to get more mind-wracking.