Scorpion is a clone created from Peter Parker by Dr. Otto Octavius. When the Carnage experiment escaped and cell doors were opened, Scorpion decided not to stay there any longer.
Scorpion met Peter Parker when he crashed at the mall while Peter was dining with Mary Jane Watson. Scorpion started babbling about not falling for it, but the cops showed up and he sprayed them with acid. Scorpion and Spider-Man then started fighting and Spider-Man defeated him. After seeing Scorpion's face Spider-Man freaked out and grabbed Scorpion and brought him to the Fantastic Four. After Fantastic Four did tests to see who Scorpion is and came up with 94,2% match to Peter Parker, Spider-Man revealed his identity to Fantastic Four to show that he's the real Peter.
Peter freaked out again and left Scorpion with the Fantastic Four and ran away. After Scorpion woke up briefly and also freaked out, after hearing the name of Spider-Man, then Mr. Fantastic and Invisible Woman decided to call Nick Fury, and let him see Scorpion with his own eyes.
It's later shown that Nick Fury obtained Scorpion, still alive, and he ordered his men to start working on it.