When you first run Pokédex 3D, you will be prompted to Create Extra Data and will be shown some instruction pages.

Step 1: Create Extra Data

The first time you run Pokédex 3D, you will be prompted to Create Extra Data. When you do this, some space will be used up on the SD card.

Step 2: Read the Instructions

You will be shown some basic instructions on how to complete the pokédex using the Give and Get buttons. Slide the stylus toward the direction where the arrow is pointing to move on to the next page, which says that you can receive Pokédex 3D data via SpotPass while the 3DS is in Sleep Mode, although you can turn this off if you wish. The next page mentions that you can press Start to turn on the AR Viewer and point it at a Pokémon AR Marker to make a pokémon appear. The final page says that when you find Pokémon AR Markers, you should take photos to get stickers.

Step 3: Press the on-screen Start button

There will be a big blue button on the screen that says START, below the words "Everything is ready." Tap the blue button with your stylus to start using Pokédex 3D.

Step 4: Choose your SpotPass setting

A 3D pokémon will appear on the top screen, and the touch screen will prompt you to choose whether you want to receive Pokédex 3D data while your 3DS is in sleep mode. Choose whichever option you are most comfortable with. You can change it later.

Step 5: That's it!

After that, you can browse your 3D pokédex! It starts with the Unova starters and their evolutions, as well as Audino, Axew, Emolga, Foongus, Hydreigon, and Scraggy, for a total of 16 pokémon to start out with.