WMG / The Prince of Egypt

Aaron grew up believing Moses was dead.

I saw this theory over on Tumblr suggesting that Aaron, who was probably too little to really remember Yocheved sending Moses downriver, knew his mother had a baby who didn't live with them anymore; he grows up to assume this is because Moses was one of the babies killed by the Egyptian soldiers and Miriam and Yocheved are telling him this story about Moses growing up in Pharaoh's palace because neither of them can bring themselves to tell him what really happened. And this accounts for Aaron's initial reaction when Moses just shows up out of the blue.

Egypt's gods chose not to intervene during the plagues.

The gods of Egypt, pissed off at either being used cynically — the magicians were basically using them to perform parlor tricks, and without really believing in it — or being invoked to keep the Hebrews in slavery, decided to ignore all the incantations and leave Egypt to the whims of Moses' god.

Alternately...

Egypt's gods were in the middle of an Enemy Civil War

Aten (Egypt's version of a monotheistic god) made real by Amenhotep IV's worship but then forcefully eradicated from Egypt, took the opportunity to reassert his power and wreak havoc as revenge and/or Enemy of My Enemy camaraderie.

Or Alternately...

The Hebrew account left out one major detail, the war

The Egyptian Gods weren't fully outmatched by the Hebrew God. It was before the plagues that God sent the angels to battle them. So while they were in the midst of a battle, God reigned plagues down on Egypt while their gods were too busy to be able to counteract. In order to make the victory sound more effective later text made them look metaphorical and/or weak, even though it was actually a more competitive battle.

• This theory brought to you in the same line that pagan deities at least originally were flesh Nephilim. YMMV on that though.

The killings by Moses and the wandering by the Hebrews for forty years didn't happen after this movie's events

First off, Moses is not the murderer he was in the original tale of the Exodus. He's horrified by killing people and felt sympathy for the victims of the plagues. Likewise, God is far more benevolent. In the original story He would kill people for sympathizing with his victims, he does nothing of the sort to Moses in this movie.

The mother of Rameses' son is dead.

Rameses was married early on in his reign, but his queen died sometime after their son was born (possibly even in childbirth). Rameses' close relationship with his son is thus partly because he sees him as someone to remember her by, which adds another layer of tragedy to his death in the final plague.

• Actually, Nefretiri, Rameses' wife and his son's mother, did appear in the film albeit briefly. Look closely at the beginning of the scene of Moses' return with Rameses and you will see her standing at the side of Rameses' throne.
  • It's not never made clear (at least not in the movie,) that Rameses' current wife is the boy's biological mother.
  • The woman is Nefertari in theory. The historical Nefertari predeceased her and Ramses' firstborn son by a year. The Great Royal Wife after was Nefertari was Isetnofret, the mother of Merneptah. Even with this being a Compressed Adaptation in terms of Egyptian history, as Amun-her-khepshef died a man rather than a child, it is ambiguous to if the Great Royal Wife is Nefertari or not but taking Egyptian history into account, it seems unlikely.

Seti knew that Moses was Hebrew, or worked it out while he was growing up.

And yet, he still loved his adoptive son regardless. Perhaps it was because it was a case of You Are a Credit to Your Race: it was okay if just one Hebrew child survived if he was raised "right", if he was raised "properly" in the Egyptian Faith instead of the Monotheistic religion that the Hebrews had. Perhaps it was because, deep down, a tiny part of him did regret his actions, and one surviving child was a balm to the guilt. Or perhaps it was something else.

Despite everything, Rameses still becomes the man he did in real life.

In real life, Rameses II is widely regarded as the greatest Pharaoh, with a long, prosperous reign, dozens if not hundreds of monuments, and at least eighty children, before he died in his nineties. Perhaps, in the film continuity, Rameses learns from his mistakes and returns to Egypt, focusing on healing his Kingdom from the Plagues and protecting it from those who would take advantage of its weakened state. And in the process, he becomes the great man he always desired to be: it just took him almost losing everything for him to get to that point. (Which parallels Moses in that both brothers needed to lose almost everything to become their greatest selves.)

God or something kept Moses safe during the journey down the Nile

The Nile River is a very dangerous river, featuring Hippopotamuses, crocodiles, Black Mambas, Cobras, and Mosquitoes. Plus, with the fishing boats on there, some divine being must've protected Moses in his basket as he made his way to the palace. The most likely answer is God did it.

• Miriam directly says He protected Moses in the river.