In The Beginning
The puzzle involved finding the core similarity in each painting. It was solved by selecting the images containing apples.
The solved puzzle
Sixty-Four Squares
The puzzles were solved by rotating the various rings in turn until they formed an image.
The first solved image.
The second solved image.
The third solved image.
Descendants
The puzzle was solved by locating a hidden Apple of Eden in each image, under the infrared light.
The first solved image.
The second solved image.
The third solved image.
Hidden Morse and Masonic Pigpen symbols containing messages were present in the images.
Infinite Knowledge
The puzzle was solved by locating a hidden image in each photo.
The first image's location.
The second image's location.
The third image's location.
The fourth image containing an Apple of Eden.
Hidden messages were present in the images.
- Outskirts of Brest, France, 1944: On the road was hexadecimal cipher that read "Antikythera Mechanism, much older than 150 BCE."
- Beaufort, South Carolina, 1862: Above the hidden image was a Caesar cipher that read "Ancient city, Rajastan, India, irradiated by PoE."
- First pictorial representation of a gun, 900: Near Buddha's face was a binary code reading "Sumerian, Me 23".
Instruments of Power
The puzzles were solved by selecting images which shared a common theme. A sword in the first set, a staff in the second set.
The first solved puzzle.
The second solved puzzle.
Brothers
The puzzles were solved by rotating the various rings in turn until they formed an image of Cain slaying Abel.
The first puzzle required rotating Ring One 2 times to the left, Ring Two 3 times to the left, Ring Four once to the right, Ring Five 3 times to the right, and Ring Three around to complete the image.
The second puzzle required rotating Ring One 3 times to the left, Ring Three 1 time to the left, Ring Four 4 times to the left, Ring Five once to the right, and Ring 2 around to complete the image.
The third puzzle required rotating Ring One 3 times to the left, Ring Three 1 time to the right, Ring Four 5 times to the left, Ring Five once to the left, and Ring Two around to complete the image.
The fourth puzzle required rotating Ring Three once to the right, Ring Five 2 times to the left, Ring Four 2 times to the left, Ring Two 6 times to the right, and Ring One around to complete the image.
The quotes accompanying the images were taken from the Pearl of Great Price, and the Morse Code underneath the final image read "Templar texts adapted by Mr. Smith".
Keep On Seeking, And You Will Find
The first puzzle required finding the core similarity in each painting. It was solved by selecting the images containing the red shroud.
The second part of the puzzle involved scanning a picture of the crucified Jesus Christ, in search for the Shroud of Eden. The Templar insignia and the words "They took it." were hidden in the image.
Martyrs
The first puzzle was solved by locating a Piece of Eden using the sonar signals.
The first solved image.
The second solved image.
Each image contained a hidden message.
- Nicholas II of Russia: A binary cipher which read "17th July 1918", the date Nicholas and his entire family were murdered, was hidden within the image..
- Joan of Arc: Hidden binary message in the image read "30th May 1431," the date Joan was burned at the stake.
The next phase of this puzzle involved picking up the flame and placing it over the image of Joan, and placing the image of Grigori Rasputin over the image of Nicholas.
Image showing Joan's burning.
Image showing the Russian Revolution.
Hat Trick
The first puzzle involved using sonar to locate a Piece of Eden in the images.
The first solved image.
Image of Houdini's grave.
The second solved image.
Image of Ghandi's funeral procession.
The second puzzle involved solving a Caesar cipher to obtain the access code.
The solved Caesar wheel.
A message followed.
Apollo
The first puzzle involved using sonar to locate and identify the Apollo 11 landing module.
The solved image.
A Mason pigpen cipher that read "Johnson was one of them. The bee's drone too. Follow the money" was hidden in the image.
The next puzzle was solved by correctly aligning the gaps across the rings.
The solved image.
The third puzzle involved using sonar signals to locate the Apple of Eden
The solved image.
Hidden messages were present in a negative visible underneath the official image. When scanned, the flag on the landing module contained the Abstergo logo, and the white flag contained the Templar insignia.
The Inventor
A message preceeded the first puzzle.
The first puzzle involved activating all the lightbulbs across the world map.
The first solved image.
The second puzzle was solved by finding hidden images in the photos.
The second solved image.
The third solved image.
Hidden message were present in the images.
Titans of Industry
The first puzzle puzzle involved solving a Caesar cipher to obtain the access code.
The solved puzzle.
A message followed.
The second puzzle involved breaking all lightbulbs across the globe.
The solved image.
The third puzzle involved selecting the Apple of Eden held in Mark Twain's hands.
A hidden Morse cipher reading "They used it to make Tesla go insane. The organization took his research. Alien Property Custodian." was present in the image.
The fourth puzzle involved solving a Caesar cipher to obtain the access code.
The solved puzzle.
A message followed.
I Am Become Death, The Destroyer of Worlds
The first phase of the puzzle was another partially-obscured Caesar wheel. The two pictures on the left each had the key: one had the number 9 while the other had a triangle rafter highlighted. When the wheel was aligned, Desmond saw how the symbols go from triangles to squares and circles. The solution was thus:
An Abstergo memo instructed a Templar to give "O" the authorization to proceed with a real-world verification of his experiments.
The next screen presented a big red button. There were no hidden texts here, so pushing the button revealed a video clip of an atomic explosion.
The final screen presented a 'sonar location' puzzle. Listening to the sounds of the Geiger counter allowed Desmond to home in on the access code that completed the puzzle.
Bloodlines
Subject 16 was starting to deteriorate. He had visions of holding a rifle at Gettysburg, stabbing a man and getting blood on his waistcoat; of an opera soprano who cried as they copulated; and of speaking at the Forum but no one listening.
The only puzzle involved selecting the paintings with a common theme: that of the union of gods and mortals. The paintings are: Danaë Visited by Zeus, Jupiter and Io, Leda and the Swan, Cupid and Psyche, and the Rape of Europa.
Subject 16 then revealed the Assassins' abilities were the result of interbreeding between humans and Those Who Came Before.
Guardians
The first puzzle was a picture ring (of Ivan the Terrible holding his dead son). Twisting Ring Three 2 times to the right, Ring One 4 times to the right, Ring Four 5 times to the right, Ring One 5 times to the left, Ring Two 5 times to the left, and Ring Five 5 times to the right to complete the puzzle.
The next part was a map of targets murdered by the Assassins. The cursor moved over each one to complete the puzzle.
The Cavalry
The puzzle began with a letter sent to Nikola Tesla from the Assassins, warning of the Templar's plan for Tunguska. A map was then presented with various place names, but only one name marked the correct spot: Tunguska. If the cursor hit any place names other than Tunguska, the names would shuffle again. Moving the cursor over the Tunguska text revealed a portrait of Nikola Tesla and a picture of The Staff; dragging the Staff to Tesla completed the puzzle.
An anonymous memo appeared from 1908: the Templars had taken The Staff to Tunguska to conduct experiments on it, but the Assassins recruited Tesla to destroy the artifact. The Assassins knew Tesla's career had been destroyed by the Templars, and so Tesla agreed. The Staff was destroyed before the Templars could take advantage of it.
The Bunker
The Caesar wheel in this puzzle didn't simply obscure two portions: the order of the symbols in the code box was random and there were some fake symbols to choose from as well. Looking at the symbols in the wheel and counting the number of sharp vertices, a pattern could be discerned. On the image with the tank, the < symbol was shown, and between the pictures was the number 4; placing the symbol at the number 4 on the wheel aligned it correctly. The number of angles in the picture was lesser than the number given in the wheel by three angles from the number 3 onwards. For 0, 1, and 2, the number of angles were 7,8, and 9 respectively. The solution to the wheel was thus:
An Abstergo memo showed that the war had mostly gone to plan by ushering in a new order, but "H" was supposed to meet "C" with the Piece of Eden and didn't make the expected rendezvous on 30 April 1945.
Subject 16 explained that although the Templars ushered in their new order, the Assassins were able to kill Adolf Hitler.
The final part of the puzzle involved locating the Assassin emblem in a picture of the Führerbunker. Looking in the upper-right corner over the bunker entrance revealed the emblem.
On the wall of the small cubic building in front of the bunker was a hidden Caesar cipher reading "The double was killed in the bunker".
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The Caesar wheel
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The bunker image
Synapses
The first phase of the puzzle was a Caesar wheel. The key to the cipher was amongst the black & white brain images, but two necessary symbols were obscured from the wheel. As Shaun explained, the 'trees' were 'ones' and the 'mountains' were 'tens': the values of the wheel were still in order. The correct key was thus:
Desmond was then presented with an article from the inaugural issue of Biological Frontier from January 2012. This article, by Doctors Yijie Wu and PJ Traunero, described a unique neurotransmitter that appeared exclusively in humans and yet did not react to any sort of stimulation.
The second part of the puzzle involved moving the cursor over the various synapses within the picture. Amongst the nerve lines were two circular parts.
Subject 16 revealed the neurotransmitter described by Wu & Traunero reacted in the presence of a Piece of Eden.
The Fourth Day
Subject 16 advised "It happened once before. The Pieces were once part of a whole." The first puzzle was a 'common theme' picture set: selecting the five pictures revealed a depiction of the sun: Nazca Textile c. 200; Aztec Calendar Stone 1427; The Eastern Gate 1816; Book of the Dead c. 1310 BCE.; Sistine Chapel Ceiling Fresco 1512.
Finally Desmond needed to locate the Earth within the picture of the Sun. It was located just below and left of the center. There were also four unencrypted messages in the picture, indicating that "fire from the heavens" caused terrible loss of life.
Origin of the Species
The first puzzle was a picture ring: twisting Ring Five 10 times to the right, Ring Four 2 times to the left, Ring Three 2 times to the right, Ring Two 5 times to the right, and Ring One 3 times to the left completed the puzzle.
Next was a picture location puzzle. There were no hidden messages in the picture. When the cursor was held over the eye at the top of the picture an image of the Vitruvian Man is revealed, which was Desmond's target.
Desmond would now come to a Caesar wheel that had no values on it whatsoever. The clue was in the Assassin's creed that was displayed: everything is permitted. Submitting any combination of symbols allowed the puzzle to proceed.
Desmond was shown an Abstergo memo from 3 January 1997, instructing that faked fossil evidence must be planted for Tim D. White to find so the world continued to believe human evolution did not have any assistance.
For the final part of the puzzle, moving Desmond's Apple cursor over each of the bones in the hominid skeleton transmuted the skeleton into a Homo sapiens skeleton.