So as I was playing Assassins Creed: Rogue the other day I noticed that you can acquire the Sword, or in this case Swords, of Altair. I then also realized that the sword has been obtainable in every game apart from AC3, AC: Liberation, AC: Freedom Cry, and AC: Unity.(I think anyway, correct me if I am wrong. I can't afford next gen/good PC to play it so I don't know) So after a long period of putting things together I have come up with my own head-canon as to what has happened to the sword and why only certain games have had it obtainable, because I refuse to believe it is just because Ubisoft is too busy to add it into every game.
Assassins Creed 1: Altair Ibn La Ahad
Although at first it was just what the middle rank of the order received when they reached that point, Altair came to favor the sword because of its weight and design. After the death of Al Mualim Altair decided that he would use this sword as his signature weapon and that is when the legend began. Altair used the sword for a large portion of his life, until he became older that is. When he designed a unique set of armor (which would become known as the Armor of Altair at a later date) he sent his sword away with the armor, wanting it to become a legendary set among the Assassin's...
Assassins Creed 2-Revelations: Ezio Auditore Da Firenze
...and become legendary it did! When Ezio unlocked the vault that Altair's armor was locked in during the late 1400's he utilized Altair's Sword immediately. He continued to use it throughout his days training as an Assassin and became quite fond of the blade.
When the Borgia attacked Ezio's village in 1500, he thought the sword had been destroyed along with the armor. Later on that year though he found it that it had instead been retrieved by the Templar's and they were keeping it in a secret vault somewhere in Spain. After training all of his Assassin's to their peak, Ezio sent them to find the vault and take back the sword, a mission that was met with success. Ezio then used the sword through his adventures in Rome and, just as Altair before him, used it as his official Mentor weapon when he was promoted.
When Ezio traveled to Masayaf in his early 50's he left a lot of his gear behind including the sword, thinking that he would only be gone for a few months. It turned out Masayaf was under control by Templar's and that Ezio would be out of Rome longer than anticipated. After making contact with the Assassins in Istanbul, Ezio sent an Assassin to retrieve several pieces of his equipment, including the sword, from Rome. When the Assassin returned with the sword Ezio used it during his visit to Constantinople.
When Ezio retired from the Assassins he left the sword with them, although a few years later the sword was stolen from the Assassins by a turncoat and taken to the Templars. It circled around Spain for years and finally landed in Istanbul, being held there by the Templars for many years.
Assassins Creed IV: Black flag: Edward Kenway
When Governor Torres from Havana learned that Istanbul Templar's had the Sword of Altair, he asked for it to be delivered to him with a treasure fleet, saying that he would dampen the West Indies Assassins spirits by having an artifact so dear to them, however faint intervened. Edward Kenway had been pretending to be an associate of the Governor's, Duncan Walpole. When the Governor discovered this he was so astounded he completely forgot about the sword, he sent Edward to be hauled away in the treasure fleet instead. When Edward broke free of his restraints he went and upgraded his robes to his liking, afterwards he found not one, but two swords of Altair laying on the table. Apparently the Istanbul Templar's had made a copy just in case the original had been lost. Edward took both of the swords and escaped the treasure fleet. Edward used the swords for the active portion of his life with and without the Assassins. Before he sailed back to England with his newly discovered daughter he sent the swords to be taken to a far away place where nobody but the Assassin's could find them.
Assassins Creed: Rogue: Shay Patrick Cormac
The swords were safe for a time, but in the mid 1700's a member of the fleet belonging to Shay Cormac, a skilled Assassin hunting Templar, found the location of the swords. They had been hidden in Port La Joye in North America. Shay went and retrieved the swords himself, altering one of them into a dagger. Shay used the swords as a mental attack towards Assassins, for he was killing them with one of their most precious artifacts, this caused him to continue to use them for the rest of his life.
Conclusion (AC: Freedom Cry, AC: Liberation, AC: Unity, AC3)
So in AC: Freedom Cry Adewale, aside from having no interest in retrieving them, did not know the exact location of the swords, thus leaving them alone.
In Assassins Creed 3, Liberation, and Unity, Shay is very much alive and active. His death has not been revealed so that leads to only one possible solution: You cannot acquire the sword(s) in the other three games because Shay is still somewhere delivering ironic justice with them.
If the sword(s) can be acquired in a Unity DLC, or in the upcoming AC: Victory, I will add to this post or make a sequel. Until then however thank you for reading and let me know what you think in the comments!