Her pocket dimension, if you remember it from season 1. She can use it to travel, though it's a bit odd. Think how if you travel in the Nether in Minecraft, you go a far longer distance in the Overworld.
Sometimes when you're driving down a road, a bug hits your windshield. It's ugly and unpleasant, but you just activate the wipers / cleaning fluid and it's gone in a few seconds. It's just part of driving down the road. You don't dwell on it, because that'd be silly. Bugs aren't worth the time.
@ Everyone on the gunblade ...... how the hell should I know? He's a manly man, he handles it fine. If anything, I assume he fires then as the recoil occurs, he bends back, I dunno. Ask Cervantes.
Ok the group still in the Halls of time are now heading for the bridge to the Sanctuary of Light.
I had that one picture and description and that's pretty much it in a nutshell.
The only thing left is the two doors on each end of the bridge (the one in the HoT and the one entering the SoL) which they'll need to force open and then they're free to enter into the central chamber with the massive version of the emblem that was in the HoT.
So the portal can help John and Mara get to the clock, Hajime and Eve already went there...