Strange Red Footprints

Yeah I noticed that too.

SPOILERS!!!!!

Some have theorized that it belongs to either Lucy, Shaun, or Rebecca and that one of them is secretly a Templar. This could also explain why you were forced to stab Lucy in the end. Juno knew she was not one of them and had Desmond kill her.

I spent hours on this, and even kept going back to try and figure out what was going on with the footprints.

The truth is that Lucy is the one who has left the footprints. The footprints could be red for one of two reasons. (A) Lucy is actually still working for the Templar as a double or triple agent and therefore is picked up on in Eagle vision as an enemy (which doesn't seem to register in the Sanctuary). (B) Lucy's footprints are red to stand out against the darkness and to keep you guessing as to her true loyalties.

Theories are that the reason she is down there is to work on some kind of limited access network she can use a cellphone on that will block all traces to prevent the Templars from getting at her. During the time she is gone, if Desmond checks her emails, it is discovered she is corresponding with someone known as "William M". This "William M" makes a reference in an email to the fact that Lucy had contacted him via phone and had sounded rather upset.

I think there was alot of the Desmond Miles storyline that was cut for time in the game (God knows why) or unintentionally left out. Lucy's whereabouts, Desmond's waiting on the timers, and the need for all the ancestor's items Desmond finds are just some examples.

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We're a race of peeping toms.

Here's a link to an interview with scriptwriters and the question comes up:

http://youtu.be/KqMAKGL1DpM