Another Code R: A Journey into Lost Memories follows the 16-year old Ashley once more as she explores Lake Juliet. Ashley remembers a vague time where she visited before, just before her mother's death when she was 3 years old. Players solve puzzles and gather clues to try and unlock the past - finding out what's so significant about the lake.
A large portion of the game plays like a visual-novel where you cycle through text occasionally making choices which affect the conversation. However, in between conversations, you move Ashley round the camp and its surrounding areas in a 2D plane (i.e. left and right) though it allows you to change this plane at certain junctions on the path.
Throughout the game, the player come across a variety of puzzles. Some require the use of a virtual DSi (known in-game as the DAS or "Dual Another System") to take pictures and manipulate them. You also use a Wii remote like device to open door-locks by entering codes which get steadily more complicated throughout. In addition to these, there are puzzles that use neither of these in-game objects and, instead, require you to use the Wii Remote as if you are manipulating Ashley's movements (the most publicized would be the use of a water acidity testing kit where you tilt and shake the Wii remote like the chemicals and the test tube).