Following on from the original games, Pokémon Omega Ruby & Alpha Sapphire feature Secret Bases. However, these have been fully upgraded and integrated into the Nintendo 3DS hardware and software, and are now called Super-Secret Bases

To create a Secret Base, you need to have a Pokémon knowing the move, Secret Power, and take it to one of many places in the Hoenn region. These are all indicated by a small rectangular block on walls or trees. When used, the Secret Base is open and you can then go into it.

This game has a great number of Secret Base locations across the region, each with different shapes and sizes. In addition to that, three special areas are located in the game, needing Dive to get to initially, that have a lot of Secret Bases within them. You can also check on Secret Bases using the AreaNav.

One of the core aspects of Secret Bases is the ability to share your Secret Base with other players. While in the originals, this was done simply by mixing records, in Omega Ruby & Alpha Sapphire, there are two different ways to do this.

StreetPass: The first is using the 3DS's StreetPass feature. When you have this feature activated, whenever you locally pass another Omega Ruby or Alpha Sapphire player, it will download the data into your game. It's as simple as that
QR Code: The second method is to allow for you to share your Secret Base with people around the world. At the PC, you can create a special QR Code for your Secret Base, which is then saved onto your SD card for you to upload. When people scan the QR Code using the Nintendo 3DS camera, they will gain access to your Secret Base

You can also gain the QR Code by accessing the special page on the Pokémon Global Link after you have done the Game Sync. This allows for sharing of the QR Code as well as the checking of teams and locations. You can set privacy settings so friends can see it and scan.

A mainstay of the Secret Bases remaining from Ruby & Sapphire is ther ability to completely decorate your base. This is done with a variety of items that you obtain throughout the game, such as as a special gift or through purchasing at stores in the game.

This helps you to completely personalise the space, based upon your own likes and dislikes.

When you go to other people's Secret Bases, you will meet a representation of their player. There, you can interact with these players and invite them to return to your base, to help build up a special amount of Pals. Each Secret Pal has got a variety of features that are available when you speak to them, but they can only do them once a day.

Battling: The main feature is to battle the other players. The team they use is based on the team the person had when they created the QR Code for their base, or StreetPassed their base to you. The once a day counter is separate to the Special Skills.

Special Skills

• Massages: One of the special skills is the ability to have your Pokémon massaged
• Egg Nurturing: One of the special skills is the ability to make Eggs hatch quicker
• Do Some Training: Some Secret Pals will raise your Pokémon's level
• Do Some Exercise: Boosts your Pokémon's Effort Values in a selected stat.
• Make some goods: You can receive various decorations from your Secret Pals
• Gather Berries: You can receive ask your Secret Pals to clean up the base, where they find rare items: Cheri Berry, Chesto Berry, Pecha Berry, Rawst Berry, Aspear Berry, Leppa Berry, Persim Berry, Lum Berry, Sitrus Berry, Liechi Berry, Ganlon Berry, Salac Berry, Petaya Berry, Apicot Berry, Kee Berry, Maranga Berr
• Picking Up: You can receive ask your Secret Pals to clean up the base, where they find rare items: Elixir, Escape Rope, Full Restore, Heart Scale, Master Ball, Max Revive, PP Max, PP Up, Rare Candy, Revive, Ultra Ball
• Pick up Stones: You can receive ask your Secret Pals to clean up the base, where they find rare items: Dawn Stone, Dusk Stone, Everstone, Fire Stone, Leaf Stone, Moon Stone, Shiny Stone, Sun Stone, Thunder Stone, Water Stone
• Search for Treasure: You can receive ask your Secret Pals to search for treasure, where they find rare items: Big Nugget, Big Pearl, Comet Shar, Float Stone, Nugget, Pearl, Pearl String, Rare Bone
• Tell your fortune: Gives you a MAX O-Power at random.
• Bargain Power MAX: The fates want you to go shopping at once!
• Capture Power MAX: The fates want you to catch Pokémon! Right now!
• Prize Money Power MAX: The fates say you needn't worry about money!
• Full Recovery Power: The fates predict that your Pokémon will be well!

Another feature of the Secret Bases, and one that stems more from Diamond & Pearl, is the Capture the Flag option. Once a day, you can go by the Secret PC in each Secret Base and collect the flags. The more flags you collect, the higher your Secret Base Rank is. This then affects the strength of the special features your Secret Pals provide, such as levelling up, or the amount of happiness

If you have a person as a Secret Pal either through StreetPass or Passing By online, when you talk to them in their base if that player has collected flags today, you will be able to receive an amount of flags equal to the amount they have collected, up to 30 per player.