The Ending Of Stoker Explained

While India is rummaging through her father's desk in his office, she discovers an alarming secret. She finds hidden family photos of Richard, Charlie, and their younger brother, Jonathan, when they were children – Charlie's face is cut out in a few of them. Other photos from when Richard and Charlie were teenagers only show the two of them, Jonathan missing. Perplexed, India keeps digging and notices a large stack of letters addressed to her from Charlie that he has been sending to her throughout the years of his apparent travels abroad — her father kept them instead. Overjoyed and on the verge of tears upon learning of an uncle who understood her and wanted to be a part of her life, India sees "Crawford Institute" stamped on the back of every letter. 

Putting the pieces together, a panicked India reaches for her phone to call the sheriff's department. Charlie catches and corners her, asking if she wants to know what happened to Richard, to which she replies, "I'm curious about what happened to Jonathan." Recounting the details, Charlie shares that Jonathan was Richard's favorite, and one day when Richard had left the two alone together, an overly jealous and sociopathic Charlie buried young Jonathan alive. Thus, Charlie was taken to the Crawford Institute where he read every book and learned multiple languages while he was locked away, soaking up all the knowledge that he could. 

He remained at the institute until the day he had chosen to be discharged, which happened to be India's 18th birthday. Richard picked him up, and gave him money and a car to go to New York where he would be set up forever, never allowed to come back. After Charlie pleads to be taken home, in a fit of rage, he hits Richard over the head with a rock until he is no more.