Once you complete this story arc, you will then be teleported forward in time to the normal game, with your next mission being the beginning of the Klingon War story arc.
This is all contained within its own story arc exclusive to this faction of character. This brings you through several of the more famous Original Series episodes, including fighting the Gorn, battling the neural parasites, and saving the Journey to Babel mission. The TOS character goes through a prelude to the normal storyline for Federation characters. AoY DLC Note - If you plan on doing the DLC as well, and you want to save another partial playthrough, you MUST choose a TOS 23rd century Starfleet character instead of the regular Starfleet character.