Peter left Stiles (his mate!) behind before finalizing the bond, to fight the baddie himself, believing that its the only way to keep Stiles safe. Of course he neglects to mention it to him but whatever. It's Peter. He's weird and dramatic like that.
Derek mostly knows why Peter left but Peter won't speak to anyone in the pack for fear his mate will be harmed. Meanwhile Stiles is breaking, slowly crumbling inside and the new bond is pulling at his soul to find his mate and finalize the mating bond.
While Peter is off trying to keep his mate safe from afar, Stiles is getting closer to Derek [NO Derek/Stiles PLEASE!], the closest thing to his mate that will ease the bond.
Peter finally kills the bad guy but not before being nigh fatally injured. Stiles, who felt Peters pain and believes that Peter is dead, runs to Derek before the bond knocks him unconscious to give Peter strength to heal. Derek puts him in his bed and cuddles with his packmate trying to make him feel better when Peter comes home. Peter, seeing Derek and Stiles sleeping in the same bed comes to the wrong conclusion and runs, but not before Stiles and Derek wake up and see him.
And please end it with a happy Peter/Stiles