I like the idea. Hmm, maybe a rough structure:
SP4: Symbiote's discovery, intro of Eddie Brock, a bit of background on symbiote, villain is Scorpion.
SP5: Lizard is villain. Spider-Man comes into contact with symbiote when Peter went to see Doc Connors after class for some reason or another. More story for Eddie (Infinity Diem and I did a good brainstorm on this stuff).
SP6: Peter's relationship with MJ is tested by her fear of Peter and Peter's foe Venom. Venom is the only villian to die an unsympathetic death.
Very rough, needs work, obviously.