This is kind of spoiler-heavy as far as plot elements, but I'm not going to give away any big details. Mostly background stuff:
Hellboy and and Liz have moved in together, albeit at the Paranormal Lab. John Myers is no longer a part of the team, and actually they don't even mention his name in the draft I read - everyone else is back. Instead, Hellboy is chasing down some monsters and comes right across a news crew; the secret is out and the FBI has to eat crow and go public with their secret unit. This puts a lot of pressure on Hell and Liz, who were already expriencing serious problems. When Hell doesn't do much of a good job coming off for the public, a suave character named Johann is brought it. He's dressed like an old detective and has a glass bubble for a head that's filled with what looks like gas. In some weird manifestation, Johann is actually free energy, more or less, contained in a suit (I have no idea if he's a character in the comic or not).
Anyway, keeping this brief, Johann delights Liz, who's tired of Hell's brash behavior (shades of the previous film), but the gang has to team up to fight a rogue Prince. He's the son of the King of the woodland ghouls, a group of "monsters" that include gnomes, trolls, fairies, tooth fairies, and all other minor imps that roam through the forest. A long time ago there was peace between the humans and the woodland creatures, but then there was a war. To win the war the King conjured the Golden Army, a group of metallic soldiers that were invincible. Sadly, he couldn't control them, and the Army ended up killing innocent human women and children. The King split the key that controlled the Army into three pieces and buried them across the globe. Now the Prince wants the war renewed and has captured two of the pieces of the key. The last piece is held by his sister, the Princess, and the Prince is out to capture her. Unfortunately for him, Abe has fallen in love with her...so Helboy and the crew have to protect her and stop him.
So, basically, the plot revolves around Hellboy fighting off characters from fairy tales.