Mission writing is a critical piece of Thorium. Thorium is an excellent set of controls to tell stories, but it will not write the stories for you. Stories are told through a mission, a timeline of events and objectives. Missions are configured on the mission config screen which allows for automation throughout the timeline. Additionally, the FD, occasionally with help (ex. llfx, 2nd chair, auxcore...), use characters to give more details and push the story along. Missions can range from all styles, big or small. Continue for details on how to set up your mission. Determining the events themselves will be up to you.
Mission config screen shown: