 " A New Day in the Old Town " was co @-@ written by consulting producer Akiva Goldsman and co @-@ creator J.J. Abrams , with Goldsman also serving as director . In the DVD special features , actor Joshua Jackson explained the second season begins less than a day after the previous season 's finale , " so the characters have only just barely had a chance to catch their breath from all the madness in the first season , and launch right back into the second one " . Co @-@ executive producer Jeff Pinkner considered beginning the second season directly after first season 's final scene between Olivia and William Bell , but changed his mind because he thought it would be more interesting to show how Olivia 's disappearance and reappearance affected the Fringe team , as well as the rest of the season . The scene between Olivia and Bell is consequently not shown until the season 's fourth episode , " Momentum Deferred " . The premiere began the " gun arc " storyline , which commenced with Olivia hurtling out of her SUV and becoming too weak to control her gun during her physical recovery , and ended with the killing of the shapeshifter posing as Charlie Francis in " Momentum Deferred " . 
