 Eventually , Clark is forced to find all three stones , which results in the creation of the Fortress of Solitude in the season five premiere . There , Jor @-@ El informs Clark he needs to begin his training in order to complete his destiny , but Clark interrupts the training to go back to Smallville , which forces Jor @-@ El to strip Clark of his powers . When Clark is killed in his mortal body in season five 's " Hidden " , Jor @-@ El resurrects Clark with his powers ; as a result , Jonathan 's life is traded for Clark 's in the episode " Reckoning " . Clark 's consistent disobedience forces Jor @-@ El to imprison his son in a block of ice in the season seven episode " Blue " , but after learning a clone of Clark has returned to Smallville in " Persona " , Jor @-@ El frees his son so he can take care of the creature . When Clark thinks a world without him would be better , Jor @-@ El sends Clark to an alternate reality to show him the world would be worse if he did not exist in it . By the start of season nine , Jor @-@ El begins fully training Clark for his ultimate destiny . As part of that training , Jor @-@ El informs Clark he needs to tune his Kryptonian intuition . To do so , Jor @-@ El gives Clark the ability to read people 's thoughts , only to take it away at an important moment and force Clark to apply what he has learned about human behavior . A clone of Jor @-@ El is released on Earth in the episode " Kandor " , but he is murdered before he can fully reunite with Clark and is only able to share a single moment with his son before dying . 
