Apophis is the embodiment of chaos, often taking the form of a serpent. Here's how Nut characterizes him: "He hated Creation from the moment the first mountain appeared out of the sea. He hated the gods, mortals, and everything they built" (20.47).
Why is this a big deal? Carter remembers something he'd learned about ancient Egyptian beliefs: "The Egyptians thought Doomsday would come when Apophis ate the sun and destroyed all of Creation" (24.149). That's a cheery thought, eh?
One way to keep Apophis too busy to destroy the world is to keep him constantly fighting. That's where Bast comes in: she was imprisoned in the Duat with Apophis, struggling to kill him again and again. When she got out, a spell was put on the prison to make sure he stayed put. In theory.
The scary thing is, Apophis makes a gamble at manifesting in our world, and almost succeeds. Sadie notices all of the chaos rising from the destruction of the red pyramid when it takes shape. It's "an enormous crimson river at least a mile long and a hundred meters wide. It writhed in the air, trying to become solid, and I felt its rage and bitterness. This was not what it had wanted. There was not enough power or chaos for its purpose. To form properly, it needed the death of millions, the wasting of an entire continent" (40.46).
Apophis dissipates after that, but not before telling the godlings that he'll be back, and he'll get stronger. What a scary dude.