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Thaddeus is the captain of Faraday's army while Autonymus is a scientist who lives secluded west of Faraday. The game reveals that they are brothers, with Autonymus being once romantically involved with Ellie, one of the princesses of Faraday. However, sometime before the party arrives, she dies in a hunting accident while Thaddeus was acting as her bodyguard. This has a profound effect on Autonymus and he secludes himself away from everyone, working on robots in his seclusion. From this point on, Thaddeus finds it difficult to talk to Autonymus as he becomes despondent and abrasive to everyone. Thaddeus' relationship with Autonymus disintegrates from there.
Some time before the party's arrival, the country is being attacked by automata, mechanical androids from the Dark World with orders to kill the populace of Faraday. The citizens of Faraday and Frobisher are demoralised at the length of the war and the casualties. Because the soldiers of Faraday are unable to withstand the massive attack of the automata, the king has enlisted the help of mercenaries.
The party arrives to see Thaddeus hold a strategy meeting with his troops. After it is done, he leaves to go to Faraday Castle.
After the party signs up to be mercenaries, Thaddeus holds a meeting with all of the other soldiers and mercenaries. He asks them if anyone has any ideas on how to defeat the automata. One of the soldiers suggest that they talk to Autonymus because he is a mechanical genius. Thaddeus informs them that Autonymus wouldn't be interested in helping them. However, one of the soldiers conscripts the party to talk to Autonymus anyways. The party travel west to the Institute of Automatry, where Autonymus lives. Inside, he is working on a mechanical being which is named E.L.L.I.E. When the party tries to talk to him, he ignores them at first. When they persist, Autonymus becomes abrasive, telling them that he has no concern with the populace of Faraday and that he has greater compassion for automata than the people.
The party returns to Faraday Castle and inform Thaddeus that Autonymus has refused to help. Thaddeus chooses to accompany the party to speak with Autonymus. When they reach the Institute of Automatry. Autonymus rebuffs them again. Thaddeus comments that it was a waste of time coming. As the party and Thaddeus exit the cabin, a lone automaton appears. It breaks down in front of the party. Autonymus, hearing the noise, comes outside his cabin to investigate. There he sees the automaton. He and Thaddeus take it inside where Autonymus tinkers with it. Thaddeus orders the party to return to the castle because he fears that the automata are invading the castle at the moment.
As the party is fighting wave after wave of enemies, something happens to the automata. They start to attack each other. The party realises that there is a signal being broadcast from the automaton that Autonymus fixed that is causing the robots to malfunction. With this new weapon, Thaddeus feels confident that they can can invade the Automaton Stronghold.
The party heads east to the Automaton Stronghold. Autonymus and Thaddeus arrive shortly after with the restored automaton, now known as E.L.L.I.E. E.L.L.I.E. broadcasts a signal that renders the automata in and around the base unable to receive orders from their operator. As before, they malfunction and go berserk, allowing the party to continue. Thanks to E.L.L.I.E., the party is able to stop the menace caused by the automata.
The party, Thaddeus, and Autonymus appear before the king who thanks them for defeating the automata. He tries to give them a reward but Thaddeus refuses, saying that it was his duty to protect the country. Likewise, Autonymus is uninterested with a reward, leaving with E.L.L.I.E.
In the present, the Institute of Automatry is named a No Man's Land. Autonymus has been dead for a long time. His bones are lying on the bed while E.L.L.I.E. is making soup. E.L.L.I.E.'s logic is that soup will make him better, not realising that Autonymus has passed away. Meanwhile, one of Thaddeus' descendants, Ambrose, has become the present king's tutor, while Ambrose's son, Theo, is the captain of Faraday's army.
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