Warhammer: Rogue Trader is all about choices from your character’s Origin to your allies in battle and trade. One of the earliest options is between two warring parties led by Felek and Theobald. Unfortunately, you must choose wisely as you will be unable to proceed until they are both dead.
Rogue Trader gives context to Felek’s aggressive stance and Theobald’s role in the matter through lootable items, which you can use to decide whether to support one character or the other. Nonetheless, your decision could lead to a battle against both.
Felek made many mistakes during the conflict, despite him saying otherwise. Siding with him means fighting Theobald and Felek in the end. This route will result in both leaders being killed, and you will not be able to leave the station until this happens.
It’s preferable to side with Theobald if you want to fight Felek with his help. While this choice is obligatory, it doesn’t provide anything unique; all choices are roleplay-centric and provide the same rewards. You will have to battle Felek.
As a bonus, both characters will still die so you can get their rare equipment and bring the Navigator Cassia with you. The big battle will be much easier this way, and you’ll still reap all the rewards for completing the quest line. The rewards are Theobald’s Staff of Orsellio Guardian and Cassia as a companion.
After the battle, you can now leave Warhammer 40k: Rogue Trader‘s Eurac V with Cassia as a new Navigator. With all four of the control prompts leading to the same result, it is clear that this choice is just about roleplaying. There is no way to change the outcome.
Siding with Theobald at the onset will make the process easier and you will fight less. However, in the end both Felek and Theobald will die.