The story in Destiny doesn't flow right. It doesn't make any sense especially with this new expansion. Why would people be doing all this stuff to supposedly help Eris prevent Crota from awakening and by doing the strikes and story missions apparently succeeding... Only to have to kill Crota anyway? It doesn't make much sense. In a roundabout way it is just saying to people that actually look at the story to just ignore all that other nonsense because you have to kill Crota anyway. What separates Destiny from other games is there is not huge plot holes in the story. Why did those other missions fail? We don't know. We just hear Eris babbling on and on about what a great job we did killing Omnigul and destroying Crotas soul. Only we didn't because sure enough, we still have to kill Crota.
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During the wakening mission intro she says that the hive separated his soul from his body and they were destroyed after that. Like a lich you must kill his soul to kill his physical form. I don't necessarily think that it makes sense but if you listen to the intro they do try to explain that one thing at least.