For a three-act plot analysis, put on your screenwriter’s hat. Moviemakers know the formula well: at the end of Act One, the main character is drawn in completely to a conflict. During Act Two, she is farthest away from her goals. At the end of Act Three, the story is resolved.
Act One
Tom Jones is a great kid, but he is also—at least everyone thinks—the illegitimate son of absent parents (Jenny Jones and Mr. Partridge, the schoolteacher). He doesn't exactly have a fortune coming to him, and his relationship with his guardian is not totally secure. While Squire Allworthy has been raising him generously, the neighborhood generally agrees that Tom is a rascal who is going to come to a bad end.
And since Tom has no official relationship to Squire Allworthy, there is nothing Tom can do to protect himself if Squire Allworthy decides to side with the anti-Tom crew.
Act Two
Once Squire Allworthy does, in fact, side with the anti-Tom crew, Tom winds up on the road with basically no money and no set future. During this section of the novel, Tom seems about as far from a happy ending as possible: his beloved Sophia barely avoids marrying the loathsome Mr. Blifil, despite really intense pressure from her father and her aunt. Tom's supposed friend, Black George the gamekeeper, steals what little money Tom has from Squire Allworthy.
Tom keeps trying to join the army to at least give himself something to do, but he never quite gets there. And worst of all, Sophia runs away from home just in time to arrive at the same inn where Tom is in bed with another woman. So Tom is (a) disowned, (b) bankrupt, and (c) in the doghouse with his ladylove. How is all of this going to get resolved?
Act Three
Londonis like a magnet in Tom Jones: it attracts and draws in all of the characters in the book (luckily, just in time to resolve the novel's complicated plot). So, Squire Western appears at Lady Bellaston's just in time to prevent Sophia from being assaulted by Lord Fellamar. Mr. Dowling the lawyer arrives at Mrs. Miller's at just the right time to explain Mr. Blifil's horrible schemes for once and for all to Squire Allworthy.
And Mrs. Waters/Jenny Jones meets with Squire Allworthy just in time to assure him (a) that she is not really Tom's mother, and (b) that Mr. Blifil tried to use Mr. Dowling to bribe her to prosecute Tom for murder. Because all of these characters turn up when they need to, we get our happy ending: Squire Allworthy names Tom his heir after disinheriting Mr. Blifil, and Tom finally gets to marry his beloved Sophia.