His most well known work is the Tony Award winning Natasha, Pierre & The Great Comet of 1812, an electropop opera based on War and Peace.

[2] In 2008 he composed music for Beowulf – A Thousand Years of Baggage, a Banana Bag & Bodice SongPlay written by Jason Craig and commissioned by the Shotgun Players in Berkeley, California.

[3] After Beowulf, he co-created and performed in Three Pianos, a drunken romp through Schubert's "Winterreise" (with Rick Burkhardt and Alec Duffy, directed by Rachel Chavkin) that premiered in 2010 at the Ontological-Hysteric Theater, winning a Special Citation Obie Award, and had runs at New York Theatre Workshop and American Repertory Theater.

[4] His next work was Beardo, a Russian indie rock musical based on the life of Rasputin, which Malloy wrote with Beowulf collaborator Jason Craig.

Comet was commissioned by Ars Nova and premiered there in October 2012, directed by Chavkin; in May 2013 the show transferred to off-Broadway playing in Kazino, a tent custom-built for the piece, first erected in the Meatpacking District and then in Times Square.

After an extended sold out run, the piece transferred to the McKittrick Hotel, home of Sleep No More, and has since played in a number of cities, including Edinburgh, San Francisco, and Cambridge, where it won an Elliot Norton Award.

The show features an eight-part a cappella chamber choir and "explores addiction and nihilism within the messy context of 21st century technology" premiered in a limited run at the Signature Theatre Company in New York City.

[12] The middle section of the show, titled Moby Dick, Part III: The Ballad of Pip was previewed at Joe's Pub back in March 2014.