Already from a game mechanics point of view it would make more sense for Rasputin to side against the Darkness, as we obviously are getting Warmind/Russian themed armor in the next season, which seems to me to point to some sort of allegiance quest. I doubt that if Rasputin is sided with the Darkness that we'd be allowed to side with him as our first step to the Dark side.
But that out of the way, I believe we have very solid evidence for why Rasputin would not join the Darkness. While I think the Osiris cutscene was cool, I find it far fetched to tell Rasputin to choose a side. If he truly was forced into a light or dark scenario then he has far more reasons to side with humanity than anyone else. That said, Rasputin really could lend a hand as if he does not help us he is almost assured destruction.
To prove, or rather explain, why I believe he has no other option but us I'll list his basic relations with others races who may would side with the Darkness, or at least stand against the Light, and why humanity is his only potential friend.
[u]Vex:[/u]
While the majority won't actively follow the Darkness, there is the Sol Divisive. Rasputin has been combatting the Vex since before the Collapse. At Ishtar he was brought in to help combat the simulations of the Vex. This would be a logical enough reason to assume that Rasputin has no love of the Vex and vice versa, but he has continued hostile actions against the Collective into the new era.
[u]Cabal:[/u]
The cabal, while not as prominent as the Hive or Fallen when one thinks of claimants to the warmind's technology, throughout the Warmind dlc an apparent hostile link is shown between Rasputin and the Cabal, but this extends even further into the past. In the Grimoire card "Ghost Fragment: Rasputin 2" the eponymous Warmind is seen to send an orbital strike on a group of Vex and Cabal as a test of his recently awoken strength. The Cabal then cry out "Find the source!" Rasputin very apparently does not consider the Cabal potential allies, and likely would not consider Calus any better, especially with his connection to the Darkness.
[u]Fallen:[/u]
The fallen have actively sought to steal Rasputin's technology. From the Saber shank strike, to the Devils rummaging through his old vaults for SIVA. The Eliksni have shown nothing but interest in thieving from the Warmind and therefore an alliance between him and the Fallen is presumably all but impossible unless it be through humanity first.
[u]Hive:[/u]
Another faction who have actively fought against Rasputin. The entire Warmind dlc is an argument against Rasputin being allies with the Darkness. The worshippers of the Darkness have warred with Rasputin, it would make very little logical sense to enter into an alliance with the Darkness when it would likely include joining with the Hive as well.
[u]The Darkness itself:[/u]
There may be two schools of thought here. One would be Rasputin fought the Darkness before and he'll do it again, the other being that he'll join with them now that he knows the fight is hopeless. I believe Rasputin is too practical to not realize that the Darkness would not care a whit about him and would promptly destroy or corrupt him.
With guardians now as an unplanned variable, Rasputin now may see an opportunity to actually win against the Deep, erasing his biggest failure. While Rasputin wishes to be autonomous and his own master, I still believe he would want to finish what he started, even if it were a part of his original programming.
[u]Humanity:[/u]
Rasputin was created by us, which is both a good and bad thing when it comes to his allegiance. On the one hand, he's told us he is own master in no uncertain terms and the Iron Lords have fought him and advocate against him. On the other hand, his only real (or potentially real) friend is Ana Bray. The only bengs who have helped him are human, and we share all of our common enemies. There is plenty of hostility between man and machine here, but with every time we have helped Rasputin we have grown closer to an alliance.
Since the beginning of this story beat, Rasputin has given Osiris a lead to something in deeper Space. Many are still trying to make heads or tails of this, but if the tip really was helpful, then we may already be seeing further signs of cooperation.
Anyway, what do you guys think? Which side of the so very thin line do you think he'll stand on?
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Read up the Last Days of Kraken. He fired on humans because he was acting under a command directive. He's both beneficial and detrimental.