DM: Anyway, guilt-tripping aside, the journey to Canterlot goes mostly smoothly.
Applejack: Exceeeeeept...?
Pinkie Pie: Murder mystery! Murder mystery!
DM: There's a guard station checkpoint at the outer limits, and from that point on and around the entire city, there is a magical force-field bubble.
Rarity: That... can't be trivial to make.
Shining Armor: Oh yeah, I bet.
DM: The guards let the train go through without stopping. The edge of the magic barrier passes through the train and through each of you, making you feel like you've been scanned.
Rainbow Dash: Eugh!
Applejack: "Scanned"...?
Twilight Sparkle: I guess that makes sense, with Discord still technically at large... Wait, would a magical barrier even stop Discord?
DM: Based on your experience, you can safely intuit: Probably not!
Shining Armor: Wait, it wouldn't? Awww.
So in the actual cartoon episode, the bubbles is supposed to block changelings from passing through. If there were changelings on a train traveling through that bubble wall (without stopping mind you) that would mean those changelings on the train would be bug-smooshed against the back ends of the rail cars when it reaches them.
That can't be pleasant for the passengers to witness. Imagine riding the train and the mare next to you suddenly gets half her bones crushed as she is forced through the seats to the back of the car you're in.
Half? Try "all" - and the rest of her, before the bloody smear that used to be a changeling pretending to be a mare gets forced through the back wall.
Though, this being MLP, it's more likely there would be a pony-shaped hole in the train and the changeling would survive, possibly with disguise intact (though likely dismissing it willingly afterward, as there would be no further point in it).
The bubble shield was there as a defense, yes. But I don't think they were specifically scanning for changelings at that point; they didn't know who had made the threat. Where are you getting that -this- bubble (as opposed to the one at the end of the second wedding episode, where they knew what the threat was) was specifically anti-changeling?
Well, in theory is a kid show so they did not show everything but just think of the changelings when the bubble was re-formed, smashed against buildings or just crashing against the floor after being thrown to the sky by the bubble shield
It's also possible that the bubble has several "access points" (gates, trains, the usual) that scan anypony who goes theough and immediately removes any enchantments (counting changeling shapeshifting as an enchantment here) therefor laying any changelings bare.
The barrier might not stop Discord, but it would give enough warning that they could perhaps start evacuating the capital before Discord took it over. It would also give notice that the Ponyville trap had leaked, and that the rest of the world was once more in danger.
Maybe they could do that as a side story to cool down after whatever disaster happens here (and we know it'll be a disaster because Twilight is just a boatload of issues).
Given how her brother's already and reacting, I doubt Twilight's player will be at fault for the disaster.
Wonder how the "put whole city under forcefield" is going to be justified with 4e rules (probably a custom ritual), but I can already feel the gloating (which if it's a ritual I hope the DM interrupts with a "anyone who knows the ritual can do this, dude.")
Red Herrings by the Bushel.
I ran a Cluedo inspired session, and half the NPCs had motives to kill the victim. The other half had motive (and means, and opportunity) to go after the PCs as well.
The Maid did it, with the Slithering Tracker, which is hiding in the barrel of Pickled Herrings.
Or maybe that's slightly terrifying.