I defeated the boss in Fire Castle, went in to get

You will get the seed once you kill Kilroy.
Go through Gaia's Navel, and use the shortcut to get back to Watt's,
get him to power up any of the weapons that need it. Then go to the
store and stock up on any essentials, then the inn. After a good nights
rest head down to the middle of the main floor area. You will see the
Elder and Jema as well as a huge hole. Talk to both of them, and then
jump into the hole. You will find yourself on a steel ship, make your
way downstairs, and on the top-right hand side you will find a Whip's
Orb. Head into the room above, to meet the members of the Scorpion Army
for the first time, they have stolen the Water Seed to power their
machine 'Kilroy'. After they walk off, make your way into the next room,
to fight him.
Ater you have defeated Kilroy, the Scorpion Army will give the water seed
back.