With the worlds merging and Superman initially powerless, his brother Tal-Rho flies him into the sun to recharge and supercharge his cells.
In a desperate move to regain his powers, Clark asks his brother, Tal-Rho, to throw him into the sun. This supercharges his Kryptonian cells, allowing him to return with enough power to stop Ally and separate the merging planets.
The core theme of this series has always been family, and the finale doubles down on this. Jordan and Jonathan finally get their "Kent" moment. While Jordan has been the focus of powers all season, seeing Jonathan step up as the tactical leader and the supportive brother was a welcome payoff for his character arc this season.
The final shot of the "Man of Steel" Statue in Smallville being torn down by angry mobs (fearful of aliens after the Bizarro invasion) sets a very different tone for Season 3. Clark Kent losing his secret identity is a status quo shift that changes the entire dynamic of the show. It brings the "man" part of the equation into sharp focus—how can he be a father and a husband when the world looks at him with fear or awe?