In 1943, the USS Eldridge, which was located in Philadelphia, was transported to a future state for eighteen minutes with the use of a Piece of Eden.
By 1998, Daniel Cross lived in Philadelphia. That year, he was abducted by the Assassin Hannah Mueller and taken to an Assassin camp. The two of them later returned to his apartment, where they were followed by the camp's director, Paul Bellamy. After experiencing a hallucination caused by the Bleeding Effect, Daniel attempted to escape from the two Assassins, freerunning over a couple of rooftops.
Two years later, Daniel returned to Philadelphia after he unwillingly killed the Mentor of the Assassin Order. He made his way to Abstergo Industries' Philadelphia facility, where he spent time inside the Animus.
Developer Ubisoft considered having Philadelphia as a primary location in Assassin's Creed III, but decided against it because the city's grid-like planning would have made freerunning counter-intuitive. However, the city's Independance Hall does appear in-game during a cutscene.