The Inventor
This puzzle began with a letter from Nikola Tesla before giving Desmond two 'find the Apple' pictures. Unlike previous puzzles, Desmond couldn't home in on the sonar.
- Wardenclyffe Tower: Directly above the centre-most door in the picture, the image hid 3 unencrypted quotes from Tesla.
- Tesla c.1900: The Apple was in Tesla's hands. Also hidden in this picture was a Caesar cipher reading "He used it to develop a bottomless source of energy. Telefunken Wireless Station".
Subject 16 revealed that Tesla found the Fourth Apple in Croatia, but the Templars found the Apple in Tesla's lab and used it to drive Tesla mad.
For the final image, moving the cursor over each of the light globes activated them.
Titans of Industry
The first puzzle was a Caesar wheel: the key was hidden in the schematics that was also shown on the page, 4=1. The password was thus 240.
For the next map, the cursor over each of the light globe deactivated them.
The next puzzle was a 'spot the Apple' picture, showing Mark Twain in Tesla's lab. The Apple was in Twain's hands; there was also a hidden Morse cipher reading "They used it to make Tesla go insane. The organization took his research. Alien Property Custodian."
Desmond was then shown a letter from Thomas Edison to a Mr. Morgan, both Templars, discussing Tesla's intention to use the Fourth Apple to provide free electricity and information networks, against the Templars ideas. Edison thus urged Morgan to cut Tesla's funding.
Now Desmond had a second Caesar wheel to solve: but some of the symbols used on the wheel were obscured. The symbol pattern was fairly simple: dashes represent multiple dots, which represent a tally. The key to the Caesar wheel was split amongst two images: the Model T car (2) and the cover of the newspaper. The code to enter was thus:
The next letter was from Henry Ford to Edison. Edison apparently gave (or at least authorized the use of) the Fourth Apple by Ford, allowing Ford to keep his workers on lower wages. Ford was eventually instructed to give the Apple to "H," who would "take over" and begin a war that would allow a new Templar order to arise from the chaos. The letter also revealed the Templars knew H was intending to "purge" Europe and that Ford, at least, supported this idea. The letter also implied that Firestone was also a Templar.
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Solution to the first Caesar wheel
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The image map
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Solution to the Mark Twain image
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Solution to the second Caesar wheel
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.
The 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.