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Eagle Vision is the Sixth Sense.

Juno says that humans are born with only five senses, whereas Those Who Came Before naturally have six. She goes on to say that as TWCB were in decline, they attempted to pass their sixth sense to the humans "in the blood". However, she says in no uncertain terms that TWCB were not able to fully incorporate their sixth sense into the human race, saying that we "can see the blue shimmer", but nothing more.

Basically, I think that Eagle Vision is the result of TWC Bs' attempts to pass the sixth sense over to the humans. We know that it is carried genetically (Shaun, who is not of Assassin stock, does not have Eagle Vision, whereas Desmond does), and when using Eagle Visions, friendly targets turn up as covered in a blue shimmer.

Leonardo used the Apple when it was in his possession.

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!

• Leo says as much when you first meet him in Brotherhood

The 'Ones Who Came Before' are actually identical to humans, but with perfect genetic memory

Juno referred to the Sixth Sense, 'Knowledge', which humans were made without. This could easily be the ability to access genetic memory naturally. Also, according to some of Subject 16's revelations in the previous game, Desmond is likely the descendant of both a human and a 'One Who Came Before'. Since he is experiencing prolonged 'Leaked Memories', this could explain why he was the only one who could see Juno. If he is descended from her, her persona could be 'Leaking' out from his Genetic Memory. This could explain how she was able to Control him, even if she seemed to need to use the apple to do so.

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 are the 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 certainly 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.
  • I get a feeling that if the real Lucy is dead and being replaced by a fake, maybe that Lucy has undergone Becoming the Mask.
  • I thought that 16 was refering to Juno not being who she said she was
  • She could have also been brainwashed into being a sleeper agent.
  • I always thought it was a blood trail left by Ezio when he was injured.
  • You're all incorrect about the red marking line seen in Eagle Vision. It was put there in play testing because play testers away got lost in the city, and that led them back into their HQ. When they removed it in the actual game, some of the lines where still there.

Regarding Juno's reason for killing Lucy

Remember Kessler from In Famous? Basically the same thing.

Lucy is still alive.

And if so, I hope she's still with the Assassins because I don't wanna hear about rumors of her being a Templar.

• Jossed in Revelations.

The person stuffed into the Animus at the ending is not Desmond, but Lucy

We have already seen Desmond ancestors, and Rebecca and Shaun both comment about their experiences. But what about Lucy? She's a great fighter, team leader and researcher to be just a Badass Normal.

The voices at the end (not Shaun or Rebecca, so probably other assassins) claim someone's gone into shock, which again would make Lucy more probable. What if Juno manipulated the whole thing because there was important information on Lucy's ancestors, and getting her into the Animus was vital to the mission?

Thus we get the setting for the next game: To find the last piece of information, hidden in the memories of a female Assassin.

• Unfortunately, they refer to the person being put in the Animus as "he". Lucy's a girl.
• Jossed in Revelations.

One of the temples that the modern Assassins are looking for is in Turin, NY

The so called "perfect number" found in the Pythagorean Temple at the end of the Da Vince Disappearance is 43 39' 19N, 75 27' 42W. These are the lat/long coordinates of the town of Turin, NY. Given that the Ones Who Came Before knew that the animus would be developed and that Desmond would be using it to relive Ezio's life, there has to be something there that they want him or someone associated with him to find.