Really, this might spoil everything on this idea. Like, everything cool about it, anyway. I still don't know if I can figure it all out, but more ideas are coming, so, at the rate it's going...
So, Saber accidentally summoned. Has Avalon, does not have Excalibur.
Image of Saber and Shirou facing off against some kind of endless enemy.
So, maybe something like:
Magi trying to reopen Grail to Root. Go to Ryuudou because of remote location and last place opening appeared.
Waver goes under the mountain to the actual system. Why? Notes left he discovered? Talk with Shirou about things Illya once said? Pure happenstance?
Saber, Shirou, and co go to Ryuudou. Others deal with magi. SxS go voluntarily bathe in mud to confront Angra? Somehow get inside?
Confronting Angra. Takes Iri's form since Saber is familiar. Talk of Illya's fate? SxS voluntarily bathed in mud and voluntarily took on "evils of world" and going on what Kotomine said about it wanting to be born, they accept that it wants to come out and that they will face it. Metaphorically taking on the evils and removing burden from Angra? Accepting, Iri/Angra spits them back out, then disseminates into the real world as HA wolves? Even more powerful and in multitude because of mana overflow from another activation of Grail without use? They face it on Ryuudou--once again their "place of victory" while magi are forced to watch.
Waver communicates he's dismantled as far as possible, but with opening leaking out power, they have to close it on their end first. Can't do so without someone doing it from the inside--no Excalibur, only Caliburn--so Saber volunteers. The masses of Angra still present. She seems to know something, though, and after a quick farewell dives in through the opening again.
Grail opening closes, now with Angra on the outside and within "purified" insofar as it can be. Fight with Angra drags on; Shirou doesn't quite have firepower enough as UBW was cancelled to close the hole. Supposedly can't use projected Avalon because connection to Saber permanently shut, but--
Doesn't realize it during fight, but steps out onto Ryuudou lake and doesn't break surface.
Final bit of fight: so, faeries and lakes. On top of the lake. Go ambiguous--he falls to his knees, but in a splash of water pulls out sword. Traced it, or drew it? Other parts of Arthurian legend has Galahad drawing sword from stone, also sword from river. Arondight given to Lancelot. Shirou-specific sword? Or Excalibur, temporarily loaned, as Arturia now on "other side."
So, implying LE but without going there, like Escaping Fate. He's capable of wandering into Avalon not by accident, but, you know, fate. He has their blessing.