In The Beginning
Subject 16 states that "everything we've been brought up to believe is a lie" and explains he has proof. This proof has been split into 20 encrypted pieces and hidden in the Animus software as the Glyphs.
The puzzle to solve involves finding the "core similarity" in each painting. Identify and select the pictures with apples: The Fall, Hercules in the Garden of Hesperides, Atalanta and Hippomenes, Judgement of Paris and Idun and the Apples.
Sixty-Four Squares
You must solve 3 picture rings: spin the various rings in turn until they form an image. The centre circle of the puzzle is fixed, so work you way from the inside out. Sometimes rotating the thickest circles first makes understanding the correct positions of the smaller ones easier.
Each picture is of a famous historical leader who held an Apple of Eden during their career. These leaders are Queen Elizabeth I (Piece #2), Napoleon Bonaparte (Piece #1) and George Washington (Piece #3).
Descendants
You are presented with a series of pictures, which you will see normally and then under a red light. When the picture is under the red light, you'll have to search the images for the hidden Apple of Eden. While you're searching the paintings, you will also uncover some hidden Morse or Mason Pigpen symbols that contain a hidden message.
Apple #3 is located just below Roosevelt's knee.
On the blackboard you will also find a Pigpen cipher. This text reads "The Masons brought it across the sea. George Washington passed it on".
Houdini beginning the Chinese Water Torture cell escape, 1913
Apple #1 is located below Houdini's head, on the water torture chamber.
Above Houdini's feet you'll find a Morse cipher that reads "They hit him in the stomach".
Gandhi during the Salt March, 1930
Apple #2 is located atop Gandhi's staff.
Another Morse cipher is hidden in this picture, reading "The bullet hit him in the chest".
Infinite Knowledge
Like the previous glyph, you need to find the Apple of Eden in each photo.
Burning Viet Cong base camp, My Tho, Vietnam, 1968
Look inside the bazooka barrel on the soldier's shoulder. There is no hidden cipher text in this picture.
Outskirts of Brest, France, 1944
Check around the kneeling soldier's helmet, on the far side of the street.
On the road you will see a hexadecimal cipher that reads "Antikythera Mechanism, much older than 150 BCE".
Union troops in formation, Beaufort, South Carolina, 1862
The Apple is located atop one of the bayonets, slightly right to the centre of the photo.
Above the Apple is a Caeser cipher that reads "Ancient city, Rajastan, India, irradiated by PoE".
First pictorial representation of a gun, 900
The final Apple is in the upper-right corner, in the hand of a demon.
Near Buddha's face is a binary code reading "Sumerian, Me 23".
Instruments of Power
Solution: For the first puzzle, select images containing swords (Perseus, Greece; Attila the Hun, Eurasia; Sigmund, Norse; King Arthur, Britannia; Joan of Arc, France). For the second, select images containing Staves (John the Baptist, Jerusalem; Alexander the Great, Macedonia; Shabataka, Egypt; Peter, Jerusalem; Moses, Egypt).
Information: Subject 16 explains how many famous warriors of antiquity, such as Atilla the Hun had possession of the Sword of Eden, and how wise men such as Moses possessed the Staff of Eden, and that these relics were passed down through the generations.
Brothers
Solution: For the first picture, twist Ring One 2 times to the left; then twist Ring Two 3 times to the left. Twist Ring Four 1 time to the right, and Ring Five 3 times to the right. Then spin Ring Three around to complete the picture.
For the second picture, twist Ring One 3 times to the left, twist Ring Three 1 time to the left; then twist Ring Four 4 times to the left, and twist Ring Five 1 time to the right. Then spin Ring 2 around to complete the picture.
For the third picture, twist Ring One 3 times to the left, twist Ring Three 1 time to the right, twist Ring Four 5 times to the left, and twist Ring Five 1 time to the left. Then spin Ring Two around to complete the picture.
For the fourth picture, twist Ring Three 1 time to the right, twist Ring Five 2 times to the left, twist Ring Four 2 times to the left, and twist Ring Two 6 times to the right. Then spin Ring One around to complete the picture.
Information: The Templar Emblem is revealed to be the "Mark of Cain," showing that not only was Cain the first Templar, but that Abel was actually killed due to his possession of a Piece of Eden. The Morse Code message reads as "Templar texts adapted by Mr. Smith." This, and Cain exclaiming that he is "Master of Mahan," implies the Mormon version of this event is true, or, at least, the most accurate.
Keep On Seeking, And You Shall Find
Solution: In the first puzzle, look for the four paintings with Red Robes, and the one painting with a snake and tree. They are: Joseph, Egypt. c. 1700 B.C.E.; Jason, Greece. Prehistory; Jesus Christ, Jerusalem. c. 30; David and Goliath, Valley of Elah. c. 970 B.C.E.; Christ Disrobed, Jerusalem. c. 30
In the second puzzle, highlight and ID the area to the right of Jesus' legs. A beeping sound will alert you when you are close.
Information: 16 reveals that Jesus Christ possessed a Piece of Eden, called "The Shroud," that gave its user the power of resurrection; he was killed by the Templars in their attempt to gain possession of it.
Martyrs
Solution: You need to select and ID certain portions of each picture. Use the beeping sound as a guide to the exact location where you need to scan.
For the first, look around the center of the staff; for the second, search the lower portion of the sword. Once that is done, use the cursor to pick up the flame and then move onto the Joan of Arc painting in the lower left. Finally, move together the remaining two images in the upper right to complete this glyph.
Information: The photo of Czar Nicholas II has a message written in Binary that reads "17th July 1918." This was the day the Czar and his entire family were murdered. There is another Binary message on the painting of Jeanne d'Arc that reads "30th May 1431;" the day she was burned at the stake.
This glyph reveals that the Templars stole the Sword of Eden from, and then killed, Jeanne d'Arc. It also states that Rasputin stole the Staff of Eden from Czar Nicholas II. Without the staff to control the populace, the Russian Revolution occurred.
Hat Trick
Solution: Find the hidden objects in two pictures then crack the code.
Move the cursor over Houdini's abdomen to reveal a hidden Piece of Eden and scan it. You'll hear a heart beat race as you get closer. Then move the cursor over Gandhi's heart to reveal another Piece of Eden. Scan it. Lastly, enter the password 312 to complete this puzzle.
Information: According to the letter, JFK (John F. Kennedy) was planning on expanding the franchise to all citizens of the United States (likely referring to the Civil Rights Act of 1964), something the Templars opposed, prompting them to kill him and take his Piece of Eden in one fell swoop.
Oswald was trained in the use of the first two "Pieces of Eden," which he used to make a "Phantom" in order to create a distraction (the phantom was made to appear on a part of the map marked with an X; the infamous "Grassy Knoll"). The letter also poses another man being in the conspiracy by the name of "Z", possibly Abraham Zapruder.
Apollo
Solution: Solve three puzzles. First you need to find the hidden lunar lander. It's located out in the blackness of space, just to the lower left of the moon.
Then you have to complete a spinning image puzzle. Twist the rings in the follow order (inner ring is called Ring 1, outermost ring is called Ring 5): Twist Ring Five 6 times to the left; twist Ring Two 4 times to the left; twist Ring Four 3 times to the right; twist Ring Three 5 times to the left. Then rotate Ring One around until the puzzle is complete.
Once that is done, find the Piece of Eden which is hidden in the shadow of the flag on the left.
Information: A Pigpen Cipher reads "Johnson was one of them. The bee's drone too. Follow the money." "Johnson" likely refers to Lyndon B. Johnson, John F. Kennedy's Vice-President and immediate successor. Him being "one of them" seems to imply he was a Templar. The title of the Moon photo reads "Apollo 11 photograph released to public." Underneath it reads "Original unreleased negative." When scanned, the US Flag contains the Abstergo logo, and the white flag contains the Templar Emblem. This means that the Templars went to the moon for some reason, likely for a Piece of Eden.