It probably made sense on paper. I mean, in the script the weirdly-edited assemblage of random shots with the tiny model of Ian falling off the paper-mache cliff, the other tiny model of Ian sliding along the cut-out diagram of the tunnel, and the real Ian suddenly falling into shot on a random set we've never seen before was supposed to be Ian surviving the deadly fall to find himself in just the right place to stop the Dalek bomb by blocking the shaft. The shots of Susan and David doing, um...something, somewhere, with stuff...that was supposed to be them sabotaging vital control systems. And the final explosion of random stock footage...that was meant to be a massive volcanic eruption caused by the Dalek bomb exploding too close to the surface, an eruption that took out all the Dalek saucers in the world, because they just happened to be right overhead, while not at all touching the Doctor who was maybe a few hundred yards away...I did stress "probably", right?
But as filmed, it's barely coherent. I don't mean, "It didn't hang together as a piece of drama." I mean, "Many of the scenes as shot and edited do not form a visual narrative in any sense of the word, leaving the viewer to guess at key plot points at what is supposed to be the climax of the story." I complained about the end of the first Dalek serial not living up to expectations, but at least you could actually tell what was happening on screen. Here, there's way too much that the audience simply has to interpolate. It's an unmitigated disaster, even before you start wondering whether every single Dalek on Earth was really gathered in the same place, let alone whether all the other Daleks in the universe are just going to give up on their big plan now that a few of their saucers have been destroyed.
But let's face it, nobody cares, because we're all paying attention to the last scene. It's equal parts gorgeous and infuriating--on the one hand, the Doctor is incredibly patronizing to Susan, simply taking the decision out of her hands by leaving her behind without giving any consideration to whether she has something with David that will truly be deep and lasting or whether he's consigning her to a life of misery on an alien planet billions of miles and millions of years from home. (For all that John Peel deservedly gets hammered by the fans for 'Legacy of the Daleks', his portrayal of Susan and David's relationship as something less than a happy ending was pretty believable.)
On the other hand, the Doctor is doing what he does from a position of love and understanding. He knows that Susan wouldn't leave him behind even if her heart broke in two from the decision. He knows that a moment like this would happen some day, and that the longer he keeps her with him the more she'll grow to resent it. He knows his granddaughter, and he knows that the right thing to do is to take the decision out of her hands. It's possible to see both of those things in that scene, because everyone involved takes the script and brings out every wonderful nuance of it. (The scene where Carole Ann Ford stares at the space where the TARDIS once was, and you realize she's never seen it dematerialize from the outside before, is a triumph that makes you wish they'd given her something to do on the series before now.)
And so the series changes. Susan is left behind, and with it the idea of the Doctor as someone with a family, someone with a home. Someone human. He's finally free to become a wanderer, completely and fully. The show is now fully free to remake him as a character, and the process of shedding its old skin really kicks into gear here.