I was scanning an older post- the one titled "Eternal Life" and I was blown away by Lhaaheim's find about the prophecy and it's relation to the finale. She found these answers on Wikipedia. Thanks Liz!!
Here is what she wrote:
The prophecy applied to the Alias storyline: "This woman here depicted will possess unseen marks. Signs that she will be the one to bring forth my works. Bind them with fury, a burning anger unless prevented at vulgar cost this woman will render the greatest power unto utter desolation."
Sydney possessed unseen marks in her gift for three dimensional problem solving, which may fulfill the spirit of the prophecy. The letter is fulfilled by three actual physical anomalies mentioned by Rambaldi that Sydney possessed: DNA sequencing; platelet levels; and the size of her heart. At SD-6 she was directly responsible for bringing forth the works of Rambaldi by collecting them for both SD-6 and the CIA. Jump to the series finale where the culmination of collecting the Rambaldi artifacts (binding Rambaldi's works) has led Arvin Sloane and Sydney to a face-off. After Jack Bristow is shot by Arvin Sloane, Sydney displays a "burning anger" by brutally shooting Arvin Sloane. This sequence of events triggers "the greatest power" storyline.
The greatest power which Sloane and Irina Derevko are both seeking is that of immortality. The greatest power is "rendered unto utter desolation" because it is forever lost. Arvin is trapped forever in Rambaldi's tomb under rock and Derevko dies while trying to retrieve the last remains of the "greatest power" contained within the Horizon device.
Sydney unfortunately had pretense in climbing the Mt. Subasio in an effort to disprove she was the Chosen One. In the end, Rambaldi accurately predicted that Sydney would ensure his greatest work of immortality would never be used again. However, in the series finale Sydney and Sloane go inside a cave in Mt. Subasio, Sloane is in possession of a Rambaldi artifact (the amulet), moments later the sun rises and shines through a hole in the cave's wall. When the rays of sunshine hit the necklace it reflects something in the wall, but before Sydney is able to see what it is, Sloane shoots the ground around her and she falls... by doing this the prophecy is fulfilled: "never having seen the beauty of my sky behind Mt. Subasio"... with "the beauty of my sky" he referred to what the sun rays would reveal, and "behind Mt. Subasio" meant inside the cave.