In 2012, Connolly replaced Brad Copeland as the screenwriter for remake of the film Flight of the Navigator and is currently the screenwriter for an upcoming Pixar film with Teddy Newton. Connolly was listed on Variety's Ten Screenwriters to Watch in 2012.
Connolly often collaborates with director Colin Trevorrow, who directed Saftey Not Guarnteed. He also co-wrote Jurassic World with Trevorrow, and is currently slated to write the screenplay for Star Wars IX with Trevorrow as director. In August 2015, Connolly was hired to rewrite Kong: Skull Island for Universal Pictures and Legendary Pictures.