"He wants to kill Noah Bennet's adopted daughter, the otherwise virtually indestructible cheerleader Claire (Hayden Panettiere). For reasons that are too complicated to explain quickly, her survival is key to thwarting the explosion (hence the slogan, "Save the cheerleader, save the world.")"
She shamed Nathan into thwarting the explosion.
Was that so complicated?
No wonder some people find Lost "too confusing."