How to beat every boss in Phantom Hourglass, including the battles at sea. Each temple boss leaves a Heart Container behind, and most also leave Sand of Hours for the Phantom Hourglass.
Temple of Fire, Isle of Ember. Weapon: Boomerang.
Blaaz splits into three flaming skulls marked with one, two and three horns. Your sword can't hurt them. Draw a single Boomerang path that hits them in order: one horn, then two, then three. They merge back into Blaaz, who is stunned for a moment. Slash him as many times as you can; spin attacks work well. When he vanishes, watch the top screen to see where he'll reappear, and stay out of the shadows of falling rocks. Repeat each time he splits until he's beaten.
Reward: Heart Container. Leaf, the Spirit of Power, joins you.
Temple of Wind, Isle of Gust. Weapon: Bombs.
Three spots on the floor make cyclones. When Cyclok hovers over one, throw a bomb into the cyclone so the wind carries it up into him. He drops to the ground; slash him until he gets back up. Watch his shadow to tell which cyclone he's over. Avoid his charge and the small cyclones he sends after you. He gets faster as the fight goes on.
Reward: Heart Container and 2 minutes of Sand of Hours. Neri, the Spirit of Wisdom, joins you.
Temple of Courage, Molida Island. Weapon: Bow.
Crayk is invisible, but the top screen shows the view through its eyes. When you can see Link in that view, it's facing you; shoot an arrow toward it. When it's hit, it pulls into its shell. Attack the shell (bombs work well) until it breaks. If Crayk grabs you, rub the stylus back and forth to break free. Once the shell is gone, hit its face or claws so it covers up, then run behind it and strike the blue spot on its tail. Its small Crayklings drop hearts and arrows when you defeat them.
Reward: Heart Container and 2 minutes of Sand of Hours. Ciela regains her power as the Spirit of Courage.
Ghost Ship. Weapon: Sword.
This is a game of tennis. Stay near the south end of the court. Three of the sisters fire beams while the fourth throws a ball of energy. Step out of the beams and into the thrower's line, then hit the ball back to her. Each sister takes two hits. With fewer sisters left, they pass the ball between themselves first, so keep track of it. The last sister throws three balls at once; only the solid one can be hit back, and the fakes split apart. Hit her twice to win.
Reward: the Ghost Key and a Heart Container.
Goron Temple, Goron Island. Weapons: Bombchus and Bombs, with Gongoron's help.
In the first half you control both Link and Gongoron. Tap Dongorongo with Gongoron to ram into its side until it falls over, then send a Bombchu from Link into its open mouth. Do this three times and the north door opens. In the second half, Link fights alone: when Dongorongo inhales, throw a bomb into its mouth, then hit the blue crystal on its back while it's down. Sidestep its fireballs and repeat.
Reward: Heart Container, 2 minutes of Sand of Hours, and the first Pure Metal, Crimsonine.
Temple of Ice, Isle of Frost. Weapon: Grappling Hook.
Gleeok has a fire head and an ice head, both wearing masks. Use the Grappling Hook to stretch a rope diagonally between two of the wooden posts, so that when one head breathes at the rope, the blast bounces into the other head. Three hits on each head crack its mask. Move off a rope if a head tries to bite it. When waves wash across the floor, stand on a post or walk the rope, and watch for falling ice. Once both masks are gone, a head will stick its tongue out before it breathes. Grapple the tongue to pull the head down onto a post, then slash it. Repeat until Gleeok falls.
Reward: Heart Container, 2 minutes of Sand of Hours, and the second Pure Metal, Azurine.
Mutoh's Temple, Isle of Ruins. Weapon: Hammer.
Keep moving around the arena to dodge Eox's arrows and the shockwaves from his fists. Hit a springboard with the Hammer to launch yourself into the air, then smash the red pegs on his stone armor. Break the stone off each part of his body. Then four more red pegs appear on his front; you have to hit all four in a single leap. Eox collapses, and his head hops after you, sometimes firing arrows. Lure it next to a springboard, launch yourself onto his head, and strike the crystal on top. Repeat until he's destroyed.
Reward: Heart Container, 2 minutes of Sand of Hours, and the third Pure Metal, Aquanine.
The bottom of the Temple of the Ocean King. Weapons: Phantom Sword, Grappling Hook, Bow.
Weapon: Cannon.
Bellum takes over the Ghost Ship and attacks Linebeck's ship. Fire at the eyes on the sides of the ship (your map shows which are open). Shooting the slime balls it fires can sometimes restore your ship's hearts. Then destroy the three main eyes inside the ship. The game asks you to save before the last battle.
Weapons: Phantom Sword and Phantom Spheres.
Bellum possesses Linebeck. Stop time with a Phantom Sphere, run behind Bellumbeck and attack. When your swords lock, rub the stylus back and forth to knock him back, then hit him quickly. When Bellum's eye opens (watch the top screen), stop time again and slash the eye. When he swings, dodge and hit him after his attack. When he starts spinning back and forth across the deck, counter with your own Spin Attack.
Giant Eye Plant: guards the waters around Molida Island. Keep the ship moving, shoot down the spiked seeds it fires, and fire the cannon at its big eye whenever it opens.
Massive Eye: traps you near Goron Island; your ship can't move during this fight. Shoot down the yellow energy balls and flying eyeballs, and hit each of its six eyes twice: the first hit turns an eye pink, the second closes it. When all six are closed, it dies.
Jolene: the pirate ambushes you after the Temple of Courage. Keep your distance. When she pulls back for a big lunge, step aside, then hit her while she recovers. When your swords lock, rub the stylus back and forth. Eventually she drops her sword and leaves. She challenges you again later in the game; that time, after you knock her sword away she attacks once more, and the next hit beats her.