Instead of filling in the answers for the questions AC2 left it just seemed to open even more questions.
XileLord
You can't sell the next game by answering all the questions in this one.
Seriously, though, like an above poster said, AC:B was not necessitated by the AC storyline as the writers initially imagined it. But when you have a game that sells like AC does and you go to your publisher and say, "we're only gonna do one more," that probably doesn't go over well. AC:B is a completely unnecessary side story that was written into the series so they could sell an extra game. That's it. It's padding to make a few more dollars off the franchise. This sort of thing happens with fantasy/sci-fi books all the time with similarly disappointing results.
As to why Lucy was stabbed. Well, it's clear that Desmond's bloodline is a hybrid of that ancient race and their human slaves. The purpose of these hybrids seems to be to preserve the ancients and return their bloodline to the world at some point in the future. I think Juno senses that Lucy is a threat because she is not the other half of the bloodline that Desmond is meant to join with (Eve) and that's why he is forced to stab her...so he can't fall in love with Lucy and delay the return of the bloodline or dilute it.
To another point - Juno's ability to control Desmond through a recording is unremarkable in the sense that previous games explain that control of humans is achieved through genetic engineering and not any sort of mind control. AC2 explains that humans were engineered on a genetic level to respond to the POE. Think of humans as golems and POEs as control rods. The POEs simply activate a dormant set of neuro-transmitters in the brain designed to subvert the will and enourage subservience, iirc. Because of this, it is unnecessary to have an intellegent being present to control Desmond - something as simple as the right radio signal will suffice. In fact this is the basis for the satellite that the Templars are launching in December.
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