This will be a bit long, so have patience.
First, lets go with the Jeremy/Katherine issue as it is very much related...although I'm afraid I must keep one key piece of information out till the end due to the following subject: Silas and his "Heaven's Gate".
It really should've been brutally obvious that Jeremy would die once he was the person to kill Kol AND more importantly the news "got out" to others besides Klaus, in the Originals family, who did the final deed. There are two prime suspects and as usual I really don't think Katherine had too much choice in the matter of what she did to Jeremy. Granted she still very much could be doing this for her, "looking out for myself...", attitude. But, I'm not convinced, not with these writers and quite a few episodes left to go.
Katherine needed some extremely good information to get to Galen, Hayley and put all the pieces together...more I think than just following them, perhaps. It might just be that this IS entirely Katherine's doing, but I'm worried that when Klaus caught his little hybrids doing bad things, he then went and found a certain werewolf girl (who just so happens to be in Klaus's new show). She could've then relayed Katherine's whereabouts which Klaus would find extremely amusing and most likely would have hunted her down quickly and found a HUGE surprise waiting for him.
He got Katherine and Galen. Then he learned about everything, including Silas, the cure, the mission of the five, the location, and then decided to force Katherine with compulsion to do his bidding--to go get the cure, at the cost of her own life or others if necessary...as Klaus is most likely scared of the damned thing (and if true, he got some great laughs out of Tyler's threats).
Time will tell, but the dangerous part is that, really ANY of the Originals that have been left behind could've helped set this up, including Rebekah; and we know how much she hates Elena.
With their brothers death, for all we know the command may've been given to end Jeremy's life, a brother for a brother--Rebekah and klaus both would enjoy that. Rebekah has also been doing everything in her power to torment Elena: having sex with Stefan, making Elena into the bad guy--to several people, but she DID save her life (but set her up to make sure Elena was no where near the cure's location, along with snapping Stefan's neck...more proof? Is she doing it herself...did she figure out Hayley's little plan, but wanted to punish her brother and also make him WANT family again--or is she in league with Klaus? Having the sword's info far in advance, with it being hidden in a very easy to find place, like he wanted it found...). But, is Rebekah planning on killing Damon in front of Elena (while forcing her to turn her emotions back on, if it's possible to override the sire bond with an Original) then finally Stefan and her?
Elijah is of course out there as well and could've stumbled across Katherine as well, also finding out about his brother's death. He also would exact revenge ONLY on the person that killed him. So are any of the Originals involved in this farce or is it all Katherine.
Finally, the shorter portion that helps tie this together.
Silas wants to open up the plane of the living to the spiritual plane. Now he said it would revive ALL supernatural beings, which would bring a world of hurt upon literally everyone in the show...hell on Earth... Or will the gate only remain open a short while with a select few, close enough to the opening (I'm guessing those closest located to where the gate opens, a.k.a. Mystic falls) allowing all the den vampires to roam back, the burned witches, Bonnie's ancestors, the Original family, Vickie, Jeremy, the little vampre Jeremy had a crush on and her mom, everyone...Tyler's dad too (although, perhaps you need to kill someone first to be considered supernatural), possibly even Stefan's best pal, and one more possibility Tatia. On the plus side Klaus gets his unsired siblings back *snicker*. But, if they ALL come back...Kol and his brother's entire line will come to kill them... Qetsiyah and Silas's lover back as well? Is Silas's lover supernatural at all?
Needless to say it would be crazy and the end of this season and the next will be, needless to say...hilariously crazy. If this much anger is released on Mystic Falls who will protect them, the witches, will Silas help if Bonnie brings his lover back?
Now for the reason I think the top two might be happening to some degree. We have a new show coming out with Klaus headlining of course: The Originals. But how fun is a show with one invincible brother (we'll see, if Katherine is acting alone he may find himself in a tight spot--literally asking his family for protection), a distant honor bound brother on vacation, and a sister who currently is FULLY disowned (which is WHY she may be the one getting the cure, to get "back into the family" and therefore making the series work--she's also turned her back on Kol, basically). To me it makes sense that atleast to some extent Silas's spell will work (and Jeremy WILL come back, he is in the credits still for some reason--unless he's a ghost like Elena was in the books) and by working all of the Originals will be restored BUT Alaric, because technically Elena is dead--so he is too and also no longer supernatural...
Anyway, I'm sure I may've missed a few details, so hack away at this and agree with what you like and don't. Personally I'm unsure of a lot of it except that the Originals will be restored to some degree due to the new series; three may just be too small of a number. Also there HAS TO be a way that Hayley gets worked in (possibly on the Originals good side, right now she's a dead woman).
I'll add more if I think of an error or other avenue of possibilties, but these are all just-for-fun speculations. So we'll see what pans out.