Why is Tom depressed?

There are two main reasons for Tom's depression. First of all, his conscience is still nagging him to tell the truth about what happened to Dr. Robinson that terrible night in the graveyard. Tom knows he must do the right thing and confess to what he saw, but he's too scared of what Injun Joe might do to him.
Secondly, Tom's hopelessly lovesick. He's developed a massive crush on Becky Thatcher, but she's got sick and has stopped attending school. Tom fears for the worst, and his depression gets so bad that Aunt Polly cooks up some unusual home remedies to try and snap him out of it. Surprisingly, they work, but not in the way intended. Tom gives one of Aunt Polly's medicines to the cat. The poor animal starts running around like crazy and creates a huge mess everywhere. Tom's spirits are duly raised.
But he only really starts to feel better when Becky Thatcher recovers from her illness and returns to school. Unfortunately for Tom, she's not feeling particularly friendly towards him, and she gives him a good talking to before she storms off, leaving poor Tom feeling utterly dejected.