When things go bad in Beantown, top assassin Killer Bean is called to clean-up the mess. Detective Cromwell finds himself in the middle between Killer Bean and mob boss Cappuccino.
Exiled artist and poet Mustafa embarks on a journey home with his housekeeper and her daughter; together the trio must evade the authorities who fear that the truth in Mustafa's words will incite rebellion.
An orphaned boy raised by underground creatures called Boxtrolls comes up from the sewers and out of his box to save his family and the town from the evil exterminator, Archibald Snatcher.