Where 'WILLARD' ended... Ben begins. And this time, he's not alone!

A lonely boy named Danny Garrison befriends Ben, the rat leader of the swarm of rats trained by Willard Stiles. Ben becomes the boy's best friend, protecting him from bullying and keeping his spirits up in the face of a heart condition.
However, things gradually take a downward turn as Ben's swarm becomes violent, resulting in several deaths. Eventually, the police destroy the rat colony with flame throwers, but Ben survives and makes his way back to Danny. The film closes with Danny, tending to the injured Ben, determined not to lose his friend.

Ben, a rat trained by shy Willard Stiles, turns on his master after being betrayed by him and induces his many rodent followers to murder Willard. After Willard's tattered corpse is discovered, an anxious crowd gathers around his Los Angeles home, and Detective Cliff Kirtland and his assistant, Joe Greer, lead the investigation into his death. They find Willard's diary, detailing his friendship with Socrates, another rat, and Ben, but refuse to release the document, which describes how Willard trained the rats to kill his overbearing boss, veteran newspaperman Billy Hatfield. Ben, who is silently observing the men, has instructed his family to hide in the old mansion's walls. While waiting for health department officials, policemen Kelly and Reade guard the house, and Reade wanders into the cellar where Willard had trained his friends. Reade deduces that the animals are hiding in the walls, but when he rips out one panel, Ben instructs them to kill the policeman. Kelly runs in too late to help his partner, and after surveying the remains, Kirtland gives Willard's diary to Hatfield. The next day, at a nearby house, Eve Garrison and her young brother Danny, who suffers from a potentially fatal heart problem, spend the day together as usual. Ever since the death of their father, Eve has stayed home to care for Danny while their mother Beth struggles to maintain the family business. In his "workroom," a small building close to the house, Danny plays with his beloved marionettes. As Danny begins to eat his lunch, Ben approaches through a hole in a screen, and Danny eagerly shares his sandwich with him. Danny, weary of his enforced solitude, is delighted to learn that when he speaks, Ben understands him. That night, Ben leads the rats on a raid of a food delivery truck, terrifying the driver into hitting an oncoming car. The next day, a policeman notifies the Garrisons that exterminators will be coming through the neighborhood the following morning to install traps and poison. Danny tells his sister and mother that he has a new friend, a rat, but Eve dismisses it as evidence of the boy's active imagination. Eve playfully comments that maybe it was Ben, the leader of the rats in Willard's diary, which has been published in Hatfield's paper, and Danny, who likes the name, decides to use it. That night, Danny composes a song about his friendship with Ben, which touches Eve. Later, Ben and his army, now thousands strong, decimate a supermarket before they are discovered by a night watchman. Ben then leads his followers into the sewer, where they have made their home in a huge, disused room reached via an abandoned tunnel. During the day, Ben again visits Danny's workshop, where Danny puts on a show for him with a rat marionette. Cuddling Ben, Danny shows him the newspaper story about the supermarket raid and warns him that he will have to be more cautious in order to evade capture. Winded after playing Ben's song on his harmonica, Danny shows his furry friend the scar from his heart operation. Danny then watches as the exterminators place traps and poison around the Garrison home. He demonstrates to Ben what the traps are, then releases him in a nearby alley, after which an older, bigger boy, Henry Gray, begins to torment Danny. Infuriated by Henry's attack on Danny, Ben and his followers bite the boy's legs until he runs away. Danny is cheered by his protectors but later that evening, when Kirtland and Greer question him, Danny maintains that Henry fell into a rosebush. When Danny mentions Ben, he cunningly brings out the rat marionette to make them believe that he has made up an imaginary friend. Back at the office, Kirtland and Greer wrangle with a city engineer who maintains that they have searched over two hundred miles of sewers, and that it will take several days to finish their survey of the sewers. While Kirtland is insisting that the search be completed immediately, Ben and his army invade a cheese shop next to a weight loss spa, thereby terrifying the occupants when they swarm through the spa. Another day, after Danny plays with Ben and some of his friends, he asks Ben to show him where they live. Danny follows as Ben leads him down a storm drain and through the tunnels to the room containing thousands of rats. Although the animals' first instinct is to attack Danny, Ben chides them and they fall back. After complimenting Ben on his house, Danny, gasping for breath, struggles home. He hears on the radio that the police are expanding the campaign to destroy the rats, and when Ben and several others appear at the window, Danny gratefully tucks them into his bed. When Eve checks on Danny, she finds the animals sleeping with him and reacts in horror, after which Beth calls Kirtland and Greer. Although Danny refuses to reveal Ben's whereabouts, Kirtland intensifies the search of the area's sewers. When two workers descend into the sewer near Ben's lair, Ben orders his followers to kill them, although one man escapes. Soon a huge assembly of construction workers, police and fire fighters arrive, led by Kirtland and Greer. Using the engineer's maps, they determine that the rats can be driven by flamethrowers and water hoses to an abandoned distribution tank, where they can be drowned. Danny, alerted by roving police cars ordering residents to remain indoors, rushes out and slips into the storm drain to find Ben. Eve follows, although she quickly gets lost as she searches for her brother. As the workmen descend, Danny finds Ben and begs him to flee. Telling him he loves him, Danny follows Ben's directions to leave and is found by Eve. The two eventually find their way to the street through a manhole cover while below, Ben's rats fight vigorously. As the workmen flee, the frustrated Kirtland and Greer go below to appraise the situation and are able to rally their troops enough to overcome the rats' organization and ferocity. After the rodents are killed, Kirtland and Greer discuss the situation with Hatfield, and the policemen admit that they have never faced such determined adversaries. Hatfield opines that all any creature wants is room to live, while at the Garrisons', a sobbing Danny goes to his workroom. Crying over his rat marionette, Danny hears a squeak and sees the wounded Ben, who has managed to escape the carnage. Overjoyed, Danny gets a first aid kit and gently tends to Ben, promising him that they will get well together.