[b]Vanilla:[/b]
1) We still don't know who the Exo Stranger is, who she is talking to, or what she is doing.
2) We know nothing about the Vex's origins, their motives, or their leaders (besides Atheon).
3) We don't know what the Darkness is (and neither does Bungie atm).
4) We don't know anything about the Traveler's true nature or origins.
[b]The Dark Below[/b]
1) Omnigul can undo her death, given the right conditions. We don't know what these conditions are, therefor it may be possible for other Hive to do the same. This means Crota and Oryx could potentially return as future adversaries.
[b]House of Wolves[/b]
1) SIVA being used to resurrect and improve notable Fallen foes means the same could be done for Skolas at some point. Combined with the Vex tech he used, he could be immensely powerful the next time we fight him (probably worthy of becoming a raid boss).
[b]The Taken King[/b]
1) Oryx's Ravenous Heart is now in the Touch of Malice, which will be seized when the Cabal kick us out of the Tower. He could still return.
2) We still have the Crystal containing a piece of Crota's soul. Maybe we could turn this into a weapon too? If we do, I hope it's a sword like the one Crota wields in Crota's End.
3) Eris Morn leaves the Tower between the conclusion of The Taken King and the Cabal Invasion. She's out there doing something, but it might be a while before we find out.
4) The Awoken Queen is MIA. Presumed dead in-universe, but we know she's alive somewhere. Personally, I hope she comes back in disguise, so we don't realise that it's her at first.
5) The Queen's Brother is off doing something with the Fallen, but we don't know what.
6) Taken are still an issue. Cabal from Red Legion are being Taken, this means they have a new leader with the power to Take. A bit too soon for Oryx's return, likely someone else.
[b]Rise of Iron[/b]
1) SIVA still exists, it's still a problem, and the Fallen may not be the last to abuse it.
2) Aksis wasn't the one in control after he Perfected himself. Someone else was pulling the strings, and besides Rasputin (highly unlikely) we have zero suspects.
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Have I missed any? Please let me know in the comments!
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(TTK) Don't forget that we still don't know Osiris' end of the plan made between him, Eris, and the Queen to stop Oryx and the Darkness. In fact, we don't know any of his plans at all, just that he started Trials to prepare Guardians for difficult challenges (HoW) We also don't know what the Nine's plans are, or why they released Skolas. We know less about the Nine than we do about Osiris (RoI) We don't know why Rasputin went silent, why he didn't stop the Fallen from claiming SIVA, why he didn't reclaim control of SIVA after the Fallen integrated with it, or why he didn't do anything to stop the Red Legion from destroying all of our satellite systems and attacking the City. What is he up to? (RoI) We also don't know what's going on with the colony of pacifist Guardians that Lady Efrideet told us about We don't know what the Awoken are hiding in a facility in the Reef that drove a crew of Dead Orbit scouts mad and is worth killing trespassers over We don't know what FWC has found in their experiments with the Device or what their plans are, or the results of sending a Ghost into the Device (RoI) We don't know who Lysander's supporters inside and outside the City are or if he's managed to rebuild any of his forces. The Concordat will live on as long as he does Aaaaaand we don't know why the Tower decided that they didn't want to allow celebration of the Crimson Days in the Tower anymore (WHY U DO DIS BUNGIE?!) _________________________________________ Here are my revisions to what you've already listed: We know that what the Stranger is doing is trying to stop the Vex from defeating humanity and taking over the universe. We know that the Vex's motive is to ensure their existence in all timelines, specifically by finding a way to come out on top in all timelines. However, we do not understand their plans for doing so because their algorithms and strategies are so complex Omnigul may not be strong enough to have a sword realm, but she is a Deathsinger, meaning that she spends most of her time studying ways to prevent her own death and to kill others. Unraveling her death is a pretty simple task compared to hiding your death or creating an Oversoul as the other Deathsingers have done. When we killed her, our goal was to temporarily get rid of her so Crota would be weakened. It's already been determined that Crota and Oryx have died true deaths under all the right conditions, so cannot be revived SIVA does have the potential to find Skolas' body and use it to create a new warrior, but it cannot revive Skolas. SIVA actually kills whatever it takes over. The only reason Taniks had consciousness when controlled by SIVA is because, according to Variks' special dialogue from the Taken version of the Strike, Taniks had been mostly machine from all of his body modifications and had transferred his mind into the ship's systems, so he just moved his mind back once SIVA had reanimated it I don't see how the Cabal could revive Oryx if we couldn't. If anything they'll destroy the ToM like all the others A Crota sword would be cool, but I think we used up all of Crota's essence when disguising our scent to enter the Oryx's throne realm I agree with every other loose end you marked down