Try to brute force maybe.
This should start the script no matter what:
Code:
ExecuteScriptFile("Data/Scripts/Quests/mission_16e/Matrix_Eridan.script");
StartMission();
This is just example code, replace the Mission_16e to the mission you want to start, including the proper script.
Keep in mind: You have got to have proper SetQuestLabels and proper variables for this to work, afterall the script is expecting the player to actually be that far into the story.