He transmatted both our Guardian and himself a split second before the Dreadnaught's shockwave hit Eris's ship

Sounds about right. One more question, is it clear what the darkness's role or purpose is? Also, is ether a light substitute?

Ether may possibly be a Light substitute. If it's not, I'm not sure what else it could be. The Books of Sorrow can tell you what the Darkness's true purpose is. It believes in a universe where only the most ruthless remain. So it uses the Hive to crusade against the other races of the universe; if the race survives the Hive onslaught, they are worthy of existing

My favorite theory is that fallen were just like guardians, but know they need Servitors(sorta like ghosts) to keep them alive. My personal headcannon is that the eliksni didn't look the same at all before the traveler came. They were made into immortal husks(kinda like guardians again) But since the whirlwind, they need a new source. There's some evidence for this but nothing concrete I do need to read the book of sorrows lol