WMG: Assassin's Creed Brotherhood

WMG: Assassins Creed Brotherhood

Leonardo used the Apple when it was in his posession.

All those deadly devices that Leonardo "invented" were really technology the Apple shared with him. Remember the Borgia did give him the Apple for a short time to experiment on and now suddenly he can not only make a flying machine that works but one with a cannon on the back of it!

The Templars have infiltrated the team.

In the ending, Juno states that "The cross darkens the horizon" and after forcing Desmond to kill Lucy, says that the way is now "clear". Not only does this raise some very important questions about why Desmond was forced to do this in the first place, but it also suggests that there is something untoward about Lucy. Juno's statements suggested that she was trying to aid Desmond, and it would be fair to assume that The "Cross" referred to is the Templar cross. While this might simply be an allusion to the overarching plot of the series, it could also mean that Lucy was another Templar threat to Desmond that he was unaware of, which would be why Juno forced him to kill her. Backing this up arethe strange red footprints seen in present-day Monteriggioni when using Eagle Vision, which lead from the sewers to Lucy during the sequence where she is standing outside, watching the moon. It may be possible that this was to access some of the town's electrical equipment (given the point about Monteriggioni's power lines being fairly weak, this isn't too far-fetched) and that the footprints were due to some... waste... that was dragged up. However, this is never mentioned. There is also fact that the footprints show up in red. Think about it, what else shows up red in Eagle Vision? enemies, and messages written in blood. So, was Lucy always a Templar agent who had to murder someone and hide the body in the sewers to maintain her cover? was the victim in fact the real Lucy, who was covertly murdered while outside the sanctuary and replaced by a Templar double? was Lucy on your side all along, just engaging in a bit of covert killing without telling anyone? or was she down in the sewers for some perfectly innocuous reason, that she never saw fit to disclose to her team? If either of the first two possibilities is true, it would certianly explain Lucy's extreme dedication - In one eMail, an Assassin leader actually asks her to calm down. Why would Lucy's stress seem out of the ordinary? could she be secretly working towards an ulterior motive? maybe she's so obsessed with finding the Apple because she's working for the Templars. Considering that Desmond is the only lead they have on the Apple (and that they have an apparent habit of planting moles in other teams), it would make sense for them to try and infiltrate the one with access to the most vital information.

• If this is true, then she must be a really good spy to fool Desmond's Eagle Vision into thinking she's an Assassin. Either that or she programmed the bleeding effect in the Animus to make her appear as a friendly to Desmond.
• Eagle Vision isn't exactly magic, and it is possible and in fact very likely that it only highlights known threats, which would allow Lucy to appear as an ally to Desmond because he sees her as such. Also, Subject 16's speech at the end of The Truth mentions something about "she is not as she seems" which could refer to Lucy, further supporting this theory.
• What if Juno wants the Assassins to fail? She refers to the "Cross darkening the horizon", but she doesn't seem too pleased to see Desmond. "The way is clear" means the Assassins just lost their best agent. Either all the Ones-who-came-before are betting on the Templars or it's just Juno. The blood is from Lucy stopping Templar agents from getting to the Hideout, and she doesn't tell the others because the stress would shatter the team completely. If Lucy was a Templar agent, I doubt she would put so much work into scheduling the weekly timetable. Or something. I dunno.
• Remember, Al-Mualim appeared blue at first too.