In the mission "Siege of the Warmind" on earth, you're sent by Eris Morn to repel the hive assault on Rasputin in the Seraphim Vault. You can tell that the hive have attempted to access Rasputin just before Omnigoul appears and summons the Watchers of Crota major wizards. Just before this, however, on the computer monitor above which Omnigoul first spawns, you'll see flashes of Venus, Mars, Mercury, the Venus map, the Mars map, and schematics for vex goblin framework/bodies. [b][i]immediately after this the computer monitor flashes a red and black coding and stops displaying any information[/i][/b]
From watching the Rise of Iron trailer, it is heavily implicated that the "plague" (SIVA) is a technological virus that has the ability to infect and manipulate living organisms, as it clearly does with the Fallen that attempt to harness it. Throughout the trailer, the SIVA virus is given a textural appearance of digitalization. This is best exemplified in the scene where the Mutant Fallen Captain with the cannon-for-a-hand spawns from a red, digitalized fog. I know my imagery is not the best, but if you look into these two separate accounts, you'll see what I am talking about.
Also, while it isn't profoundly noticeable in the full, 1:47 Rise of Iron trailer, in the shorter 7 second teaser, you can hear an undeniably distinct Vex whirring noise immediately before the scene cuts away.
Combining all of that together and assuming that the virus visible in the Siege of the Warmind mission is related to or is SIVA, I believe we can reach at least one firm conclusion: The Vex are directly related to SIVA.
The Siege of the Warmind mission was an attempt by the Hive to gain access to Rasputin, but the Hive not being technological geniuses, may have activated this plague within Rasputin that he would have had to very quickly suppress, hence why Guardian intervention was so important. It's also important to note that on the screen in that mission, it is predominantly Vex controlled planets shown, along with Vex Goblin diagrams. If we take that into account with the distinctive Vex whirring heard in the trailer, I believe we can make the Vex connection to SIVA.
What does this mean? In pure speculative terms, I'll list what I believe this could bring about for the Rise of Iron DLC.
Note: I'll try to keep away from spinfoil-hat theories and only stick to ones that seem to have some evidence.
Note 2: It is much harder to speculate about Rise of Iron than it was for The Taken King, as the TTK trailer let us know that our enemy was indeed Oryx, and we knew some of his backstory, his connection into the main enemies and whatnot
Speculation begins now
The Plague is a creation of the Vex to try and infiltrate Rasputin so that they could better understand him for their simulations, as Vex technology could not mimic the actions of the Warmind. However, this plague wasn't strong enough to fully disable Rasputin, only to fuel his decision to become dormant. We know that a Warmind existed on each planet, and Rasputin displays Mercury, Venus and Mars - all Vex controlled planets - on his mainframe computer monitor thingy. Perhaps the Vex were able to disable other Warminds with this virus, but not Rasputin.
To me, this could also be a reason why the "Charlemagne's Vault" Raid Area was eventually cut from the game: we weren't ready in terms of the story. If Charlemagne and all the other Warminds are no longer active - as the story leads us believe - maybe this is why. With planetary Warminds inactive, the Vex are free to control and manipulate the planet as they wish. I think this next expansion will bring some clarity towards the Iron Lords, but I think from a storyteller's perspective, it will begin to tie together some of these questions we have had for so long.
SIVA doesn't seem like the type of thing that would've existed early on in the game's development, but perhaps it was added later on, because if I am correct, it could bridge a lot of gaps and answer a LOT of questions.
Feel free to shoot down my theory, add in and take away parts, but I believe these distinctive clues and pointers the Bungie storytellers have left give us a strong enough breadcrumb trail to come to this conclusion.
TL;DR The Dark Below alludes to connections between Rasputin and the Vex that we see again in Rise of Iron trailers. The plague was created by the Vex to infiltrate Warminds across the system so that they could understand them. The plague wiped out the Venus, Mercury and Mars Warminds, but Rasputin survived.
EDIT: Added images depicting the two instances of the plague's appearance
This is my first lore post, so let's see how this goes. Again, feedback of any sort is welcomed and appreciated. Contributions to this theory would be great.
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Definitely the best SIVA theory I've heard so far. Additionally, Vex have red (like the SIVA) dots in their bodies so perhaps the Vex are the SIVA.