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Just make sure you tell your companions to wait in another area before opening that door first. Strangely once the conversation is complete, he still doesn't attack.
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Once you kill all the fiends and open up the door to the room which Motor Runner is occupying, do not shoot and you can still start a conversation with him to complete that quest even with him and the 2 dogs clearly dotted red on your radar.
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Same thing happened to me when i was doing the same quest. You can still complete the quest even though Motor Runner is displayed as an enemy on your radar.
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