So about the Jardaan. Pacing and Presentation

They saved the Jardaan  for a future installment, maybe. They were relevant to the whole story RE: vaults, angaran, non golden worlds, scourge - but who they were was left till the very end and then we got no details other than something happened and they left and woohoo merdia.

There probably was damage to the nexus it was just not brought up. The focal point was stopping archon rather than wondering about nexus. Technically it was  hyperion that was attacked so nexus might have been fine. Remember that Hyperion is separate from nexus but attaches for lack of a better word.

Space magic is how ryder gets disconnected. It's not really explained in a meaningful way that I recall but space magic causes a disconnect between sam and your ryder then archon uses sibling for sam. Ryder doesn't die because he/she has had the course of the game to adapt. But it does seem to put him/her at risk at the time of the initial disconnect when he is on the Jardaan ship. It looks like pressing on could kill him but nope. Just makes it harder. Ryder controls the remnant with the help of Sam. Space magic. Explained by saying that you understand the way the Jardaan think or something like that (archon's words I believe at the end portion when holding sibling I think). Kind of like a cypher as best as I understood. Remember the cypher we got from the thorian in ME1 that by ME3 we understood  all that prothean stuff in From Ashes dlc? So ryder controls the remnant because on some level he understands how to. Best guess is that because SAM understands how,  he understands how or something like that. That's how I understand it anyway. SAM deciphers the language on habitat 7 and pops acts on intuition as best as I can tell in that scene. 

Remnant were created by Jardaan. They are a layer of defense it seems to protect vaults and on their ships and all remnant tech. Yes Jardaan tech is remnant. Anything remnant is Jardaan.

The scourge is created from some kind of detonation, an attack that appears it was mean for the Jardaan or their tech anyway. That attack when mixed with remnant tech becomes the scourge if I understand it correctly. We don't know by who. That's another mystery. We don't know why but can speculate that somebody didn't like what they were doing. They did take over an entire system and terraform it then populate it with their creations (angara). Maybe they don't do this for noble reasons or maybe they did it before somewhere else and  someone didn't like that. Who knows really? Can only guess. Could even be another race they created attacking them for all we know. Anything really is possible. 

Whew...i'm glad i'm not the only one that felt this way. i too was completely put off by the whole Jaardan mess. Everything just fast forwarded so fast and quickly during the end there with the Archon on Hyperion,... attacks everywhere etc. But you just have to roll with it because.....narrative...

And Greysen, Excellent post!... i understood more of what happened in your explanation than what was actually being presented in the game at the time....

Yeah. What we got wasn't even a revelation on the lines of zomg the v Reapers are intelligent starship...or...the Reapers are harvesting all organic life to save it. No...the revelation will come later.

I HATED the way the Jardaan were introduced. It all goes back to the lackluster toning and pacing of the story in this game.

I had zero fucking idea what a Jardaan even was. Just like OP, I was confused like "wait, I thought we were talking about the Remnant? Is this a Remnant base right? Is Jardaan a new word for Remnant that the developers just decided to throw in here out of the blue?"

It was done so casually, without any sort of interest from the characters themselves that I could literally assume they were just using a new word for the Remnant and not discovering a new God species

Man, that really bothered me. It was like the game was TRYING to insult my intelligence. Like "Ohhhh. Of Course... it was the JARDAAN! Oh you've never heard of then Jardaan? Anyway moving on".

Seriously, wth

The presentation of this whole fundamental narrative arc is probably the game's greatest failing. The original trilogy played out plot revelations with such clarity and grace that you almost took it for granted.

The artificial creation of the Angara was a fascinating plot point that could've led to all sorts of interesting philosophical ramifications. Instead it's instantly put to but bed with platitudes about the Angara still being the same proud people they've always been. The original trilogy was so good at keeping the stakes high and in the moment whereas Andromeda is always lowering or smearing them, both with the overall writing and the bargain bin quippy Joss Whedon dialogue.

LOL - kind of like when the Citadel was moved to Earth? The first time I got to that part in ME3 I was like "what?"