Was playing a game on co-op with my fiancee and her friend, the friend had to leave so me and the fiancee continued without her.
After reaching the end of Fort Joy and speaking to Malady we discovered we hadn't taken the friend's character through the area to grant the Godwoken abilities and were unable to progress further. Trying to go back and do it via the statue or via Malady warping the character there results in the respective god for that character being non-interactable so we are stuck with no way to unlock those abilities and progress further.
