@thestralpony  
The Frenchies did it by taking an armory. Now we have “Bastille Day”. French military and guard were trained, but too vastly outnumbered.

@Cirrus Light  
It’s not an assumption when the story straight up tells you. The story thus far straight up says that all they’ve been doing is waiting for Twilight to return things back to how it was before all this madness happened. How would training to kill ponies benefit them if everything really did just magically go back to how peaceful and nonviolent it was before? It wouldn’t.
 
Also, you can’t just assume that they’ve been training for the day that they would rise up to try and kill the most OP pony in Equestria when there isn’t anything that shows or even talks about it happening. All that is given to us is that the resistance is very good at hiding, Twilight is not only OP but batshit crazy and that the resistance has been waiting for everything to go back to how it was before. Nothing else as of this page.
 
We don’t see any ponies training, wearing any kind of armor, carrying any kind of weapon or working on any means of defence. So far Spike is the only one in the resistance that’s even shown to have a weapon and it was recently destroyed by acid. If the resistance just shows up wearing armor and brandishing weapons of all kinds when they go to fight Twilight and her army of professional soldiers, then it’ll just be completely out of place. Nothing up to this point in the comic even suggests that they have anything like that at their disposal.
 
Their best chance to kill Twilight right now would have to be a stealthy sneak attack while Twilight is sleeping to even sand a chance. Not some army of pedestrians with shovels and pitchforks storming the castle.
 
Although I’ll admit, it would be funny to see an army of pedestrians storming the castle with shovels and pitchforks and actually win. Equestria thus far doesn’t seem to have the most competent Royal Guard training program. lol

@thestralpony  
Well if there is a Dr Who precedent, then I can’t really argue against that. I wouldn’t like it (the whole “time rewriting itself” sounds like some silly, dramatic way of an author covering something that seems illogical), but I guess I can’t fault a crossover comic for borrowing from its source material.

@Exedrus  
You forget that this is basically a Doctor Who story. And as the good doctor would point out, you can still die in the future even if the past claims that won’t happen.
 
Time would just rewrite itself so that they mysteriously disappeared before Twilight even got that prophecy and that Twilight was just waiting for them to turn up again. Thus making the reason why they disappeared in the past was because they died in the future.

@Cirrus Light  
>Kill her friends, and by the prophesy, Twilight will die just as soon if not sooner…
 
Eh, I dunno about that. By the history we know of Twi and company (they grow old together), it seems pretty clear that they can’t die here. They have to make it back to their original timeline and continue living with Twi. The mane 5 kinda have temporal plot armor here.

@thestralpony  
You’re entirely assuming they haven’t been training or infiltrating. There’s no reason to assume that. I think what he means by “time to act” isn’t that they’ve been doing nothing, it’s that they haven’t tried to kill Twilight yet.
 
 
@thestralpony  
Because her friends aren’t dead now. They died before, but they’re alive again, so it would seem this counts as an extension to their life. Now, I don’t interpret the prophecy literally, but a lot of the characters have, so they would probably realize that the life span of her friends sets a maximum on the life span of Twilight. Kill her friends, and by the prophesy, Twilight will die just as soon if not sooner, and her friends are a lot easier to kill than an alicorn tyrant.

The fact that these ponies have just been sitting on their collective asses waiting for things to go back to normal means that there’s no way they could do anything at this point.
 
It’s not like the countless hours they spent running away from danger over the last seven or so years is going to help them kill anyone. Spike is literally about to lead lambs to the slaughter right now.
 
This is just a thought Spike but maybe you should have spent some of that time training your resistance force to be able to actually do anything combat oriented instead of just having them do nothing and “wait” for years on end.

@Cirrus Light  
If the prophecy said that Twilight won’t outlive her friends, then how would killing AJ, RD, Pinkie, Fluttershy and Rarity achieve that?  
The story already established that they have been dead for a long time. If them dying naturally didn’t do anything then how would killing them now make any difference? The only way for Twilight to not outlive her friends at this point would be if she was killed by the resistance. And I stress the word “if”.

Lot of sadness and anger

You know, “the resistance” is almost always the good guys, and they kind of are, here, too, but it’d be a really neat twist if their plan to assassinate Twilight was to kill all of the keys, since “Twilight won’t out live her friends”.
 
Consider; Stormtroopers aren’t necessarily evil; many are probably conscripted and forced along, just as “innocent” in many senses as any of the random civilians. Or consider all the lives on the Death Star. But the audience still roots for The Rebels because “it’s for the greater good”.
 
Now imagine the mane six are those victims of “for the greater good”…
 
It’d sure make an interesting twist when they have to flee the Resistance for their lives, and Twilight saves them (since they thought she was evil, but she’s actually all cocoon’d).