Yeah, I'm disappointed in this outcome. Jeph could have done some excellent things with this character and this set-up but chose to just use it as window-dressing for a hand-wave of the whole dilemma. I guess we need to move forwards but I'm sorry to say that this was one of his worse arcs because of how it was handled and how it was resolved.
For once, I think you and I are in pretty much agreement. I was immediately interested by this storyline and the incredibly diverse story options it presented. Having your own memories being held captive by a third party who uses it to control you is a really cool idea. Adding the twist that the memories were bad and undesired, but still wanted, gives an extra little twist that makes this a top-notch setup, the kind of stuff that really great sci-fi stories are built off of. How do you stop someone like that? How do you beat her? Comparisons could be made to abusive relationships, blackmail, even slavery, but none of them are perfect fits because it's such a cool, unique situation.
Then creepy robot lady showed up, and I was like 'Oh, so you're just going to solve the problem through that, okay'. It felt kind of hand-wavey, since these creepy robots had never been seen or heard of before, and yet were immensely, even unfathomably more powerful than all of Hannelore's connections, who we've seen in the past to have cartoonish amounts of power.
When they brought up Emily, though, I was more along the lines of, 'OH! That's kind of neat! Because you've established that she's also absurdly smart, so they'll be using her skills in combination with theirs in order to do the hack!' It was still a bit of a letdown since it was such a quick unravelling of the original concept, but it was a neat idea.
Now, though? Emily didn't actually do anything that a middle-schooler with basic motor skills couldn't have managed, the actual quest inside Bubbles' brain wasn't particularly deep or interesting, and the final reveal was hugely anticlimactic. At this point, the story is basically over - Bubbles has no reason to continue working for Corpse Witch. In fact, Bubbles has no reason not to go to the cops and turn Corpse Witch over, or simply just go down to the skate park and use her military-grade chassis to beat Corpse Witch into a scrap heap.
Barring some extra twist that fixes everything, (And I don't honestly think Jeph's skillset includes masterfully intricate plot twists, seeing as his stories have never actually used any,) I just don't see this story resolving itself in any satisfying way. At the very least, I'm not interested in what's going to happen next, because it's just a question of what method Bubbles wants to use to go through anger management.