so basically, partridge is red john. he is not dead. he is a forensic scientist and he is very smart. so he used another member of tyger tyger to fake his death and by actually killing them, fabricating evidence and making sure the autopsy confirmed it was him, he is able to hide his true existence. he has friends everywhere, and so this could be very possible..

 he has been laying low and obviously he wouldnt hand himself into jane, so he made mcallister pretend it was him, as jane kind of suspected him, when red john is actually still out there. 

if this were to all come together in the next episode, i will be very happy.