On rereading Assassin's Creed: Project Legacy more closely lately, I came to two startling conclusions regarding Altair's Apple, which as we know from the glyphs in Assassin's Creed II came into the possession of Queen Elizabeth I of England: John Dee and Edward Kelley looked after what was presumably this Apple in the Czech Republic, and Dee later gave Kelley's stepdaughter Elizabeth Jane Weston this painting of the queen and the Apple with Juno, Minerva and Venus.
The data dump shows Elizabeth and Johannes Leo, her husband, attending a performance of A Midsummer Night's Dream by William Shakespeare, where she becomes fascinated by the parallels between the faeries and the gods of Greek myth. Why is this relevant? What could Ubisoft imply, other than that they wanted somewhere to tribute the Bard in their celebration of history? Dee told Elizabeth he found the play a "rather 'illuminating' experience": could Shakespeare, a favorite of Queen Elizabeth, have come into contact with the Apple? It may explain in the AC universe how Shakespeare was gifted with such an extraordinary talent (just as Leonardo da Vinci conceived of a tank after Ezio's Apple of Eden was activated).
Meanwhile, Ghosts of Christmas Past shows that while Charles II of England was in exile in Breda, he received letters with "a strange seal" (so probably not a Templar cross then) from someone who informed him:
It took exactly 7 years, but the usurper [Oliver Cromwell] is dead. It is only a matter of time before Parliament recognizes you as our legitimate ruler. Be patient, my lord.
The usurper's son and successor [Richard Cromwell] is weak and powerless, but we must tread carefully. He will abdicate within the month. I give you my word.
It is with great pride and greater joy that I write this letter. General Monck has effectively seized control of London. He will soon write to you. I, your loyal servant, advise you to heed his counsel."
So 1) we can speculate the Assassins killed the fanatical Cromwell, 2) undermined his son as Ezio did and 3) the Assassins collaborated with Monck to later give them the Apple, as Charles glimpsed at his coronation (in the subsequent memory). Of course, it could've been the Templars who undermined Cromwell and restore the Crown with Monck, but don't argue for that by assuming the Assassins are inherently republican, or that Ubisoft wouldn't depict Cromwell as a villain.
It's lovely to see Ubisoft planted seeds for possible games or comics about England, and that this series is a gift that keeps on giving.