Mission Marker Tokens are used by some scenario instructions. They can't be used for anything by themselves.
The Core Box Hero Atticus Blackwood's Level 2 ability also uses "Marker Token" to mark a temporary effect. There are no tokens in the game component list called just "Marker Token", so either the Mission Marker Tokens are used for that also, or you can use any other tokens not used by the scenario for that.
Mission
Most of the gameplay time in Chronicle X is usually spent playing Missions, which is essentially a tactical combat game ("dudes on a map").
Mission setup
Before a Mission can start, it needs to be set up. This usually involves building the Mission Map from Map Tiles, and placing Item (Spanner), Hazard and Door tokens on the Mission Map.
In Conquest Mode, the Mission Map is built by one or both players, depending what type of Mission they are playing next.
In Narrative Mode, the Mission Book describes how the Mission Maps should be built. Often, the Mission Book specifies at least some of the Map Tiles to use by code name (a letter, or a digit, or a combination of a letter and a digit). Map Tiles not specified by name are chosen randomly from among Map Tiles with similar background art, when possible.
When the Mission starts, the Hero Players choose two Yellow Squares to use as their deployment points, unless the scenario has already decided which Yellow Squares should be used for that purpose. Then the Hero Players place two of the Heroes on each of those Yellow Squares, and then place the other Heroes on Squares that are Adjacent to the first two Heroes.
Then the Overmind Player similarly chooses Yellow Squares for use as deployment points if the scenario hasn't already made the choice, and places Blip Tokens there. The Blip Tokens may be placed up to two steps away from the chosen Yellow Squares.
Mission gameplay
Gameplay during the Mission alternates between a Hero Players Turn and an Overmind Player Turn.