Matt Bird writes all sorts of nonsense, but he dedicates a large chunk of his time to writing game walkthroughs.
In case you hadn't noticed, Ni no Kuni is a game of fetch quests. The main storyline is full of fetch quests, the side quests are almost all fetch quests, alchemy requires a ton of fetching . . . but few of these little scavenger hunts have proven quite so important as this, the hunt for the pieces of the Clarion. Oliver needs three ingredients to bring the legendary horn back to life, and the first, he's told, is with the Cowlipha in Al Mamoon. Make it so.
Head to Lowlah's Palace
Travel to Al Mamoon and head to Lowlah's palace. She'll gush over Marcassin a bit, then, with no qualms whatsoever, she'll give Oliver a Piece of Holy Wood. Well, that was easy. She'll discuss a bit of history, then you're free to go. Ding Dong Dell is your next destination.
Visit King Tom
King Tom is apparently an expert at woodcarving, so run to his palace and pay the big cat a visit. Moments from the front door, Esther will realize that somebody has pilfered your Holy Wood! What a royal pain. Time to ask around. No one seems to know anything about missing wood until you reach the Cawtermaster's Store . . .
Find the Missing Wood
. . . where you find the Wood sitting on the owner's desk! He claims to have just bought it off a young mouse with glasses. The owner's not willing to fork the Wood over without proof of the theft, so you'll have to find the mouse and make him fess up.
Go back outside and climb the stairs near the Swift Solutions to find Tommy Stout's usual rooftop hiding spot. Up here, perched on a ledge, is the mouse. Its name is Pip, and it has some rather nasty words for Oliver. Everyone concludes that its soul mate in Motorville is in trouble, and that soul mate, Oliver realizes, is his buddy Philip. Once the mouse leaps away, use Gateway to zip to Motorville.
Go to Oliver's House
Save and run to Oliver's house. Philip is standing outside, and he's fretting over what he thinks he did to Oliver's mom. Purple light will envelop the lad, and, surprise surprise, you'll be trapped in a battle with a hulking Nightmare.
Compared to Khulan's Nightmare, Philip's Nightmare is an absolute pushover. It's slow, it's easy to predict, it doesn't hit that hard and it sits in one spot most of the time, making it easy to land a ton of hits. Its physical attacks are potent enough, and its all-hitting Rain of Terror can be annoying if it curses anyone, but overall this Nightmare can't compare to its predecessors. Defend whenever it starts to use Rain of Terror and beat it down in general. Piece of cake.
The ensuing conversation is painful, but it ends well enough when Oliver is given the chance to draw Ambition from a surprising source and give it to Phil. He'll leave, better than ever, and once Pea has had a chance to make some more cryptic remarks you can Gateway back to Ding Dong Dell.
Talk to Pip where you found him the first time. He'll be deeply apologetic for what he's done and help you get your Holy Wood back. He'll also confess that he wants to build a Cloud Sweeper—sound familiar?—and will work hard on fulfilling his dream. Good on you, kid.
Take the Holy Wood to King Tom
Take the Holy Wood to King Tom. The purring patriarch will swiftly carve the Holy Wood into, uh, Carved Holy Wood. With that done, the team has one last stop to complete the Clarion: Hamelin. Travel!
Head for the Porcine Palace. The Xanadu guard Abyssinia is still standing out front; talk to her to receive a Gustplume. Inside, Marcassin will claim to have the magical skill needed to complete the Clarion . . . but not the technical prowess. A third party will step in (surprise surprise) and help him finish the thing, gifting Oliver and company with a full-fledged Clarion. You'll also receive a new story, The Flute-Makers.
Your path is set. The Miasma Marshes await the group in Perdida. Bring an end to Shadar once and for all. . .
. . . or perhaps you could complete a few Errands before you go. Perhaps?