The objective of each agent in Inkognito is to complete a mission, together with his partner. At the start of the game, however, players don't know which mission they must fulfill!

In the standard four-player game, players guide one of four secret agents. The four characters are paired off: Lord Fiddlebottom and Colonel Bubble are always partnered against Agent X and Madame Zsa Zsa. Each of the four agents is represented by one of four figures, with different builds: tall, short, fat, thin. Only one of them represents the actual character controlled by a player. The other three figures represent spies which are friendly to them and that are trying to confuse the opposition.

On a turn, the player shakes the Phantom of Prophecy randomizer to determine his three available actions, e.g., moving on a land route or a sea route. The player moves their figures, trying to reach spaces already occupied by the other players' figures or the Ambassador. When figures occupy the same space, the current player gets the right to "ask questions" and inspect some of the cards of that player. By deduction and a logical process of elimination, they can draw conclusions as to the identity and intentions of the other players.

The first objective of every agent is to discover which of the other players is their partner. This partner has the other half of the "code" indicating their secret mission. After discovering (or thinking they have discovered) the real identity of the other players, an agent must trade their secret mission card with their ally. This will reveal the last mission and what must be done to complete it. If either agent on a team completes the mission, both players win the game.

There is another character with an crucial role in the game: the Ambassador. He may be used to get clearer information about the other characters. Everyone wants to meet him because he is well-informed and can be useful to accomplish your purposes, but he can also assist your rivals, so do everything you can to keep him far from them.

The 2013 version of Inkognito from Ares Games increases the maximum player count to five by allowing someone to play the Ambassador and move it during his turn. He can still gather clues when other players question the Ambassador during their turn, and the other players can still gather clues from him. The objective of the Ambassador's player is to know everything about the other characters, guessing their identities and builds. If the Ambassador attains "perfect knowledge" before a team accomplishes its secret missions, he wins the game.