KINGDOM HEARTS HD 2.8 Final Chapter Prologue

Secret Portals unlock after you have completed the game and saved your clear data. They look the same as the other kind of portals but will clearly state Secret Portal on the information screen when interacted with.

These portals contain a stronger version of the story bosses and can be found at the location where you fought them originally. The fights play out exactly the same as the first time you fought the bosses with the only difference being a boost in HP and attack power. Make sure you have the Support Abilities Leaf Bracer, Once More and Second Chance before attempting these and they will be more than manageable with a Balloon based Command Deck with some Cura and Curagas.

Here is a list of all locations for both characters.

Sora:

Traverse Town – Fifth District.
La Cité des Cloches – Square.
Prankster's Paradise – Promontory.
The Grid – Throneship.
Country of the Musketeers – Theatre.
Symphony of Sorcery – Precipice - place where you fought with Spellican, go on the red music portal on the Tower

Riku:

Traverse Town – Garden.
La Cité des Cloches – Square (roof).
Prankster's Paradise – Monstro: Bowels.
The Grid – Portal.
Country of the Musketeers – Backstage