Tom is the ghost boy. He was also ghost hunter Florence Cathcart's older half brother who was accidentally shot dead by his father who had gone on a rampage trying to kill Florence (Rebecca Hall) after she witnessed him shooting her mother. On seeing his son die, her father blew his brains out in front of her.
The boarding school is in fact Maud Hill's childhood home and she can see the ghost of Tom because she was his mother. It's implied that Robert Mallory might be also be able to see Tom, because he's haunted by his dead comrades.
After a jealous Edward Judd tries to rape her in the woods, Florence accidentally kills him with a blow to his head from his shotgun. Maud then poisons Florence so that her son can be with his sister as Tom apologises for scaring the boy who suffered a fatal heart attack after being left outside by Malcolm McNair.
Florence begs Tom to help save her as she's found love with Robert, while Maud kills herself to join her son. Tom comes to her aid and helps Robert save her life.
As the new term begins, Robert secretly buries Edward somewhere on the grounds, while the staff cover up the death of Maud and the haunting, while Florence remains at the school with Robert.
Thanks ND Woods!