The Templar's Order Universe is a spin-off/rewritten universe of Assassin's Creed. The changes to the series begin in Brotherhood, changing the modern day storyline and eventually the past as well.
Assassin's Creed Brotherhood
The changes begin in Assassin's Creed Brotherhood. After killing Cesare, Ezio hides the Apple beneath the Colisseum in Rome. In the present-day, Desmond, Lucy, Rebecca, and Shaun head their to retrieve it. Descending into the Precursor's temple, Desmond sees visions of a being named Juno, apparently the same race as Minerva and a Precursor. Juno berates Desmond and humanity. At last, Desmond and company find the Apple. Upon touching it, Desmond witnesses a vision of Juno creating the Apple. Lucy then stabs Desmond in the back, revealing her true Templar colors. Holding Rebecca and Shaun at gunpoint, Lucy flees while Desmond falls unconscious.
Assassin's Creed Revelations
Desmond awakens from his coma within the Animus, and meets with the conscienous of a previous test subject, Subject 16, Clay. Clay explains that due to a severe bleeding effect, his conscienous was saved within the Animus when his brain and body were fried due to overuse. Clay explains to Desmond that due to the trauma of the stabbing and Piece of Eden, his mind has nearly merged with the memories of Altair and Ezio; in order to awaken from the coma, Desmond must complete their memories and seperate his mind from theirs.
Using memory seals created by Altair, Ezio learns that Altair learned everything he could from the Apple to create a massive library. When the Mongols attack Masyaf, Altair sends Niccolo Polo to flee with the Apple, and then seals himself within his library. Upon entering the library in the 1500s, Ezio speaks to Desmond in the present. Using the book found in the dead Altair's hand, Ezio shows Desmond a vision of Jupiter, another precusor. Jupiter explains that the Precursors were destroyed by a massive solar flare, and a second solar flare will destroy humanity soon as well. Jupiter explains that everything the First Civ did to protect themselves from the flare is hidden within the Grand Temple in modern day New York.
Desmond then awakens from his coma, and explains to Rebecca, Shaun, and his father that he knows what to do.
Assassin's Creed 3
Desmond tells his father about the Temple's location, and William explains that other Assassin cells have been monitoring the site, which is being used as Abstergo to launch the final rocket in their Eye Abstergo satellite system. Desmond realizes that Lucy must've stolen the Apple to use in the rocket as the final piece necessary.
Desmond also views the memories of another ancestor, a Native American man named Connor Kenway. At the end of his journey, Connor hides his village's amulet within the grave of Achilles's son and his namesake. Desmond retrieves the amulet, revealed to have also been created Juno, and he and his team infiltrate the Italian headquarters of Abstergo, where Desmond was previously held. Desmond kills Lucy and retrieves the Apple, and learns Vidic has been transferred to oversee the final preparations for the rocket.
Calling on the scattered Assassin cells of the world, Desmond and the Assassins launch a desperate final assault on the Grand Temple with doomsday nearing. Desmond corners Vidic, who explains that the Templars knew the end of the world was coming, and planned on using the satellites in the post apocalyptic world to mind control everyone into peace. Desmond uses the Apple to kill Vidic, then arrives to the rocket itself, ready to go. Combing Juno's amulet with the Apple, Desmond places the Apple within the rocket and launches it. Desmond explains that combined, the amulet and Apple were the final plan of the First Civ to save itself from the solar flare; creating a massive shield around Earth to protect it from the solar flare.
Deep within the Grand Temple, Juno awakens. Unbeknownst to Desmond and company, the combination of the Apple and amulet has awaken and freed Juno.
The Templar Order is reeling following the destruction of their Eye Abstero satellite and loss of the Apple. Within their Switzerland headquarters, Henry Sullivan, a mercenary working for the military arm of Abstergo, relieves the memories of his ancestor, Lukas Kaster, the Templar that rebuilt the order in the 16th century and was responsible for destroying much of what Ezio worked for.