For me the most poignant moment in Rosetta is when the young fresh-faced Clark moves to the screen behind Swann and asks ‘Is that where Krypton is?’ Swann answers: ‘No. That’s where Krypton was.’
Nothing prepares Clark for this moment. He has lived, until now, in the belief that he has a point of origin: a real and physical space that exists somewhere in the galaxy. He studies the stars in his spare time and his telescope is among his most prized possessions. He longed, we suppose, to learn more of his home, to understand it and thereby to understand himself. In this way, Clark could, as a young boy, externalise his alien identity, deflect it onto his imagined ‘home’. It was an unattainable and unknowable object, distant yet always in the corner of his eye (mind).
The caves have unlocked the secret of his identity and he is drawn to them helplessly. The ringing in his ears overpowers him. Clark is curious about his true nature (he expresses this to his human parents), but there is also a force more powerful than Clark’s will at work. He hears ear-splitting noises no one else can hear. He wakes up in the middle of the road in the middle of the night. To Clark, who knows so little of his nature at this point in time, this must be a frightening reminder that he is not human and is not fully in control of himself, the two intrinsically linked.
With the truth revealed to Clark that Krypton no longer exists, he can no longer externalise his alien self. Swann tells him that he is the last of his race. Clark is alone with himself and the only other remaining remnant of Krypton: the ship. I do not believe Swann means Clark any harm, and yet his words must tear Clark’s soul apart. Swann twists the knife deeper by telling Clark that he will not find the answers among the stars (where Clark has been looking until now): the answers lie inside Clark/Kal-El himself.
Clark does seek solitude and reflection on his return to Smallville. Jonathan finds him in the cellar with the heart of the ship in his hand. However, he has hesitated to explore it on his own, suggesting that he is not yet confident acting as an individual. Jonathan, no doubt comforted that his son still needs him, suggests they do it together. At this point, the soundtrack strikes a deep and ominous note in its echo of the Superman theme. Deliberate or not, it suggests that there is much to fear in this moment. When viewed in retrospect what is to be feared in this moment is not just Jor-El’s message, but Jonathan’s presence. In the movie Superman I, Jonathan dies before Clark explores his alien identity. He reaches adulthood and makes the journey alone. Smallville’s Clark is younger and more malleable: he is more likely to respond with fear and emotion than adult rationality.
At this stage in Clark’s development we had far fewer clues about his internal life than we do now in Season 5. I am therefore speculating to some extent and this reading is highly subjective. Clark is sixteen, an age when most humans are struggling to develop an individual identity. Traditionally most teenagers move from being defined by their family to being defined by their friends. Clark seems trapped a stage behind, perhaps because his family origins are still a mystery to him. To understand them will be to gain mastery and understanding of his self, but he has just discovered a powerful absence at the heart of this mystery. He is without a ‘self’ and is defined by powerful paternal figures: Swann, Jor-El, Jonathan.
Clark asks Jonathan why he believes he is good. Jonathan replies ‘because I am your father and I know you better than anyone’. Clark still mistrusts himself and he looks to others to define him. When Jor-El’s message tells him that his greatness lies in ruling humans with strength, he interprets this as meaning he was sent to conquer Earth. Jonathan suggests that he may have ‘misread’ the message. Regardless, Clark’s immediate logic leap has linked power to oppression. It strongly implies that he already has an implicit fear of his alien nature. So far his alien self has manifested physically, both in the development of his powers and in physically drawing him to the caves and the ship. He is not in charge of this part of himself. It is something that happens to him. Jor-El’s ‘rule them with strength’ message resonates with the part of Clark that feels ruled by his alien nature.
Jonathan’s argument that he can make his own destiny is powerless against the overwhelming wall of Clark’s fear. Clark has spent his life looking for the answers outside himself. As a teenager, he has little to draw on internally that tells him he is good. Most teenagers experience self-doubt and Clark, with much of his physicality beyond his control, has more to mistrust than most. He accepts Jonathan’s hug with the air of one clinging to a life raft. Without Jonathan's presence would he have been forced to find that strength within himself? Perhaps he would simply have been broken by his interpretation of Jor-El's message. Regardless, the truth revealed to Clark in Rosetta is a scar he will bear the rest of his life, and one he was not emotionally prepared for.