I belive that because the queen is now dead, the awoken will become an enemy. Think about it. The queens brother obviously hates us, as shown in the very begining of the game cutscene with the whole getting the chordates to the black garden, and now that the queen is dead, he will probobly be king. He modt likely diden't die in the dreadnaught weapon firing, because we didn't see him die. So its kinda like darth vaders ship spinning out in star wars where he didn't actually die. So with the brother asthennew king, and him hating us, the brother will most likely wage war upon the gaurdians, and boom. Awoken are at war with the other gaurdians, and if your gaurdian is awoken, you rebel against him along with other awoken.
If this ends up happening, we could peobobly also see variks, or petra, or so eone else from the reef as a boss. Idk. I'm probobly wrong, but its just a theory.