During the 1960s, young Irish orphan Tomás (John Bell) is harassed and ridiculed for his small size, timidity, and stuttering by the other children in his orphanage.

Just after freeing a pigeon from his classroom, he is called to the headmasters' office to be greeted by Maire (Connie Nielsen).

Tomás makes friends with Nancy (Tara Alice Scully) and Seamus (Jack Gleeson).

Tomás is frightened by the bats and flees from the cave, after which Nancy and Seamus find and console him.

She discloses she was also an orphan and had similar experiences to Tomás, which caused her to choose to adopt him over the other children.

Maire teaches Tomás to picture his grandmother in his mind and he does, remembering her for the first time many years.

Alec sends a distraught Tomás home from the hospital, and later returns and informs him that Maire has died.

Tomás also learns from his friends that the orphanage will soon reclaim him, as Alec never signed the adoption papers.

He finds that Tomás's boat has capsized, but Smudge and a pod of seals push him to the shore.

'Smudge' was an animatronic, and its scenes were shot first, due to concerns about bad weather on the beach, which never occurred.