Clues are one of the main quest objects in the game. They can be gained in various ways; for example by exploring new Map Tiles.
The main use for Clues is to advance the Player Discovery token on the Discovery Track. When you Visit a Port, the UNIVERSITY action lets you trade in 5 Clues to advance the token one step. (Various effects and Traits can modify the number of Clues required.)
Discovery Track
The Discovery Track tracks the progress of the players and the enemy during the game, and also controls when a new Act begins.
At the start of the game, the Player Discovery token and the Enemy Discovery token are placed at the first space on the Discovery Track, and the Elder One Discovery token is placed on either space 8, 12 or 16 on the track depending on whether players want to play a short, medium or long game. The chosen starting point for the Elder One Discovery token counts as the end of the Discovery Track. (The Elder One Discovery token can advance towards lower numbers on the track at some points in the game, but that doesn't change where the end of the track is.)
The players win the game by reaching the end of the Discovery Track without losing the game before that. They lose the game if the Enemy Discovery token reaches the end of the Discovery Track before the players do, or if the Elder One is awakened and completes its objective.
The first time the Player Discovery token or Enemy Discovery token reaches position 4, 8 or 12, it triggers an End of Act, and then a new Act begins. Note: when playing a shorter game by choosing a lower starting position than 16 for the Elder One Discovery token, the game will end before all the Acts of the full game have started.
Note: while the normal way of advancing the tokens on the Discovery Track occurs as part of the Enemy Phase.