@CocoaNut  
Well logically killing them would mean killing her, but that doesn’t mean she’s immortal otherwise.  
Though we don’t know what they have tried until now, maybe they are the resistance’s last hope…

@armadiloeater
 
We don’t know the full extent of the prophecy, though. We don’t know if there’s more to it than has been shown or if ponies hundreds of years later have interpreted it to mean that killing Twilight’s friends = killing Twilight.

@Cirrus Light  
Actually he doesn’t need to kill them. The prophecy just says that she won’t outlive them, not that she can only be killed at the same time as her friends. If Spike really wants to kill them (or anyone else in the resistance) it would be because it’s the most convenient way, not because there is no other.

@Digitalgame  
Given my earlier comment, I think he’s lulling those three into a false sense of security to use them to win the hearts of the other two so they’ll all walk into his claws without a fight, then he could pretty much just stab them in the night.

No, this is an interesting trap:
 
Spike wants to kill Twilight, he said as much. Spike is aware of the prophesy. Then he must also be aware that he cannot kill Twilight… Unless he kills the mane five, first.

@Background Pony #84DA  
Well of course, it’s the most logical explanation, this theory has been around since the page saying that she came back from a battle changed. It’s obvious.
 
Too obvious. I’m hoping for something else, thought I won’t be too disapointed if it really is a case of impersonation. It’s a little weird that none of the characters ever bring up this possibility thought… Maybe they did? Don’t remember.
 
As for the liquid, this comic started before the episode aired if memory serves, so it’s not something to take into account.

You guys do realize that Twilight is a Crimson changling right? All of the clues and signs are pretty obvious and present. It was mentioned that Twilight came back from defeating the Crimson changling horde changed. As in a sudden personality shift. She’s become cruel and calculated, in a manner similar to Chrysalis. We’ve already seen Twilight fight battles that were out of her league and come out wiser, but never crueler.
 
There is also the matter of the liquid that can dispel the changling disguise. If spike has access to it, Twilight obviously would as well. Why would she not want it used instead of just murdering ponies? If she were actually a changling, she wouldn’t want to risk being anywhere near the stuff.
 
Finally the prophecy about not outliving her friends. Guess what? If this is a changling, that prophecy would have already been true. The real Twilight died fighting the Crimson changlings and the fake came back and likely killed her friends off one by one.
 
Obviously this is all speculation, but the pieces fit together pretty well.

You know, I’m kinda getting a Fable 3 vibe from Twilight for some reason.
 
Also, has anybody else suddenly realized their not in their original timeline?

@PonyPon  
The prophecy says, in these words: “Twilight will not outlive her friends.  
So I think it makes sense, she has not outlived her friends, yet.  
Liking where this is heading in any case.

If spike has that spray thingy to tell if they are not changelings, if that is indeed what it does, then why dont he give it to twi so she can screen everyone and make sure that no changeling can breach into the city? Annihilate the changelings and stop the slaughter.

@PonyPon  
not that it would make much sense either way.

@armadiloeater  
I might be remembering the prophecy wrong.

@PonyPon  
Well no, since it states that she would outlive her friends, meaning that if they were to die Twilight would soon follow.  
Also the prophecy still stands, since her friends were destined to come back in the future, she still has not oulived them.

@Background Pony #D385  
That sort of thing was never specified so I’m not putting much stock into it, and besides Twilight is being given her chance to win over a couple of her friends and explain herself but so far she’s kinda proving that at least some of the Resistance grievances are legitimate and not helping her case.

Wait, wouldn’t the prophecy require keeping them alive?

@Digitalgame  
they still might need to die in a certain way though, also why wouldn’t the resistance paint themselves in a better picture? You have five element bearers and very dear freinds of twilight that you could win over to your side.

Ah, so not everything is meant to seem as black and white as Spike would like us to believe… I like where this is going.

Twilight will make wure they never die.

Wait, what?

@CocoaNut  
Again, they were together for plenty of time with spike, confused vulnerable, and completely at the mercy of the resistance. The only reason they even have any idea about what’s going on is because Spike told them.
 
If he does plan on killing them, he’s letting some sweet opportunities pass him by, and again the resistance literally had to do nothing and the Iron Wolves would have most likely taken care of the group when they arrived, that they even helped puts them in a better moral standing than Twilight to begin with.
 
@Anon-a-Miss  
I’m going to take a guess and say if they are as ruthless as Twilight, they would have shown it by now, she isn’t exactly being subtle about her motives and intentions.
 
Doctor may not be omniscient but he clearly knows the major events that have taken place, he already proved he knew enough by using the prophecy to get Rarity, Fluttershy, Roseluck and himself out of jail and with a royal audience.

I don’t know what are you all talking about but I like this pic :)

@Digitalgame  
Did the resistance even know that all of this would happen? Spike and the rest of the resistance were probably just as surprised as Twilight when the rest of the Mane Six showed up. Also the Doctor isn’t omniscient.
 
Even if the resistance are the good guys, I wouldn’t be surprised if they became (almost) as ruthless as Twilight by now. Maybe they would kill the Mane Five to stop Twilight? Maybe they lied about (some of) the things Twilight did to paint themselves in a better light?

@Digitalgame
 
You’re forgetting the fact that they Gold Lily didn’t even think that they were the keys until after they defeated the wolves, they still had to be confirmed, and it’s entirely possible that the prophecy requires them to die in a certain way or all together.

Yeah, a bit late to test that theory, I mean they were never going to get a better time than just letting YOUR iron wolves do the job for them. Or baring that, any point at which all of them were gathered in one place, vulnerable and confused.
 
And even if that was true, I’m pretty sure the Doctor would have mentioned something like that.
 
You on the other hand kinda admit that you employ ruthless methods and have little empathy for those not under your rule.

If that didn’t work the first time then why would it work now?