There are 4 miss-able Ore in the tutorial area. The first is located in plain sight next to the sign explaining chests.
The second is just past that just hang a left before the long bridge and it'll be next to the watch tower. The third is being guarded by a dog behind the right hand side of the church of the town after the bridge.
And finally the last one; you'll have to turn around before entering the mines and hold right to walk back up the side of the mountain.
The mines key is at the end of the only path you can take once you find the lock.
There's one hidden Ore chest behind Yoruga underneath the stairs.

The first Ore you'll find here is next to the crashed Alien Ship. It's found after the bridge leading into the open field. Just hold left against the wall and you'll find the path upward to it.
The second is found in the cave right after the field. Hold right against the wall past the save shrine and you'll find the coffer guarded by an enemy.
The last Ore here drops from the Hayward at the Ceremonial Tree just outside of the cave.
Your weapon gained here is the Trench Gun by defeating Juli.

As you head out into the main room hold right to take the southeast door into the room with pillars ascending in a spiral. Drop into the water and head through the underwater tunnel. Hold right and you'll find the first chest with Ore in it.
Following that hold right in the tunnel again until you meet the fork and take a left and it should lead you into the room with the chest holding an Unrefined Mana Shard.
Your weapon for killing Gasha Dokuro is the Bone Riddler.

At the end of the mushroom platforming on the floor to the right will be your first Ore in a chest here.
The Cave Key to open the gate in the original room is on the far end of the mush(room) next to the ladder which also happens to have a chest at the top of said ladder.
The pool in the southeast corner leads to another chest with Ore inside and back to the gate.
A little while after passing through the gate you'll find a room with a pond with flowing water from above, behind the pond is another Ore chest.
In the room with Ru'uk's quest finale you'll have a room to the right and left with the 2 womb Keys. On the right you'll need to hit the two sacs on either side of the key to open it's door.
On the left you'll have to fight through a horde of bugs to climb up the room to where the other key is sitting.
Past the Womb Key door you'll have two boss encounters, first is the Emperor Beetle which drops the Larva Launcher and Second is the Hive Queen that drops the Garden Rune.

As with most other explanations hold right against the wall from spawn and you'll come across the first Ore chest in the level.
Traversing the left path you'll find a building, in the left rooms you'll find a Hayward and a chest with another Ore inside.
After traversing the outside mountain you'll find ruined stairs leading up to the next cavern. Holding right you'll find barrels the create a shortcut back to the beginning but heading past that is a small lava flow with a chest on the other side holding a Doll eye. You can either dash jump across, or go smack the Lava Beetle (as I've found out it's called in the artbook) to have it crawl over and work as a platform over.
Behind where the Lava Beetle was originally there is a small dark cave with an Ore chest at the end.
Similar to The Hive there's two keys you need to access the boss of the area one at the end of either path. Just a few enemies to kill or avoid.
The weapon for defeating Molten Deity is the Molten Fists.

The first thing you'll need to start opening up this level is the Keycard. Head left from the main entrance and fight past the demons. Once you're done with the cafeteria head through the right door. Take another right and you should be in a long hall way and at the end should be the Keycard.
Heading back through the cafeteria and into the machinery room there will be a door (unlocked with the Keycard) on the right with an Ore chest.
If you're here wondering about the Saipo part locations I'll have them outlined in the quest section down at the bottom.
After running through the hoops of opening doors on the right side and making your way to the top of the conveyor part of the factory the northeast most room will have the Demon Key sitting on the elevator.
You've probably turned on the wind pillars by now so head back to the cafeteria and head up the pillars to head into the lava flow tunnels along the wall. In the middle of the two will be an Ore Chest.
Head back up the wind pillars and head to the left where the vent is and on the other side of it will be Saipo and an Ore chest next to him.
Your weapon for defeating the Demon Princess in the Magma Cannon.

After the first set of arena fights you'll head through the door on the left traverse through the platforming section. You'll come up to another door with barrels directly in front of you as you open it. Behind them is the only Ore chest here. This is the only chest I felt needed an in game picture but if anyone needs in game pictures for any of the other things in the guide just ask and I'd be happy to update the guide or send it directly to you.
Your weapon for defeating Vanguard is the Railbunker.
Beating The Machine Mind gets you the Brume Rune.

The first Swamp Key will be directly behind you from spawn. Jump up the environment and you'll see a large carcass in the middle of the lake. The key is in the middle of it.Holding the right wall of the woods past the lake you'll find a breakable wall with an Ore chest inside. If you break the wall past that there's an easter egg of a little guy stomping around in circles.
Starting back at spawn simply walk out the front entrance and head slightly left. You'll see a small square shaped ruin with the chest and some ammo pots.
In the middle of the thicket of the swamp you'll find a Hayward with an Ore drop as usual.
Heading west past the Hayward you'll stumble on a huge hole in the ground with a cavern to explore at the bottom. Fight past some enemies and you'll find yourself in a foggy maze cave. Holding right against the wall will get you the third Ore chest.
At the end of the maze you'll find the second Swamp Key and the fourth Ore chest.
Again back at spawn instead of heading left head right and you'll find another cave entrance. In that first room head up and to the left for the fifth and final Ore chest. At the end of the left cave will be the start to the Ghost quest and the 3rd and final Swamp Key.
Your weapon for defeating the Leviathan is the Deepgun (called the Minigun at the shop)

This whole level is a find the colored key level so I'll be covering all the key locations in order.
The first is the Red Key, in the only room you can go in at the start right in front of you.
You'll need to head through the red door and up to the second floor and climb up the ladder to the bell on the third floor. When you ring the bell the bones blocking entrances will disappear. This unlocks the garden outside where the Orange Key will be waiting.
The Orange Key gives access to the Blue Key back inside underneath the bell room.
The Blue Key gives access to the Yellow Key on the right side of the building.
Head down the stairs of the right side of the building to find the Cyan Key at the end of the dungeon.
Now you'll have access to the Doll Eye sitting on the ground on the balcony upstairs outside from the southwest door. As well, if you continue heading to the other side through the balcony you can grab the Green Key locked behind the yellow door.
Directly underneath the green room in the dining room will be the Unrefined Mana Shard behind a Cyan door.
And now with the Green Key you can open the last two doors one back downstairs to the right of the foyer with an Ore chest, and upstairs to the right of the foyer with the Purple Key.
With that all done you'll fight the Stitched Sisters for the Syringe.

Similar to the previous to worlds you'll fight two bosses with The Dragon being the first here dropping the Bone Blade.
Taking the right path from the shrine fight past all the enemies here and if you hold left against the wall you'll come to a small cave with the first Ore chest here.
The other Ore chest is inside the crystal caverns if you take the furthest path back against the wall when you enter.
The Plague Rune drops from The Mother.

Head through the right path from the start, in the small cave past the floating creature is the first Ore chest.
When you get to the sandy seabed head directly forward past all the "circlegators" and at the other end should be a bundle of mushrooms with the Hayward of this realm on the right of them.
Holding right of the seabed, head into the skull cave entrance and you'll be in the acid pits. Climb to the top of the furthest back pools and the other Ore chest will be there.
Defeating the Second Godwyrn gets you the Wormhorns.

After doing the Yoruga fetch quest for the silver coins (check the quest section for those locations) you'll fight Ludeo to get the Tarot Cards.
In underground river is the first Ore Chest just follow it from either end and you'll stumble across it.
Heading into the tent east of the shrine holds the second Ore chest holding left and the last Unrefined Mana Shard holding to the right.

Running through the first winding battlefield you'll end up climbing a hill with a small blood fountain and at the top is a Doll Eye.
Right next to the Doll Eye is the Siege Beast Key.
The Heads of Torment gives you Torment Heads.
Past the boss is a path heading upward to blow another horn right before the horn is a circular set of steps, at the bottom of them is two chests with Ore in them.
And finally defeating Dread King Milos gives you the Arid Rune.

The first Ore chest is past the lake door. Grab the three mcguffins under the ice to open the door and head inside. Just to your left down the hallway will be where it is.
Once you get to the second shrine head down the middle path and you'll come up to a waterfall with an Ore chest in front of it.
Taking the left path will lead to a ruins with this realms Hayward dropping the usual Ore.
Continuing the left path will lead to another iced over pool, under the water is a Doll Eye.
The weapon from the Pike Shrike is the Shrike Lance.

Traverse the area as usual once you open the door next to the shrine head in and past the stairs you'll see jail cells and to the left will be a huge hole in the wall with the last Doll Eye sitting in the open.
Taking the first elevator up leads to another room with an elevator. Halfway up is a secret room with the Ore chest of this level. (And Nadia if you talked to her in 5-1)
The Astral Tome drops from the Spider Golem.

This is a huge level so I'm framing the point of reference from the gate leading to the boss. So once you've gone through the level up to that point head left from the gate. You'll be in a small room with two doors. Head into the left door and you'll find yourself in a long corridor. Continue holding left to head into the adjacent long corridor and down below are small runic enemies protecting the Private Cellar Key. Underneath the Key is also the first Ore Chest.
Climb back up to the upper level of the room and head southeast you find the room with the Master Key and the second Ore chest.
Head outside and head across the catwalk into the next room. Down in the center will be the first Gate Medallion.
Back outside jump off the catwalk and head into the Master Key door below. You should be in a cafeteria room and at the north end will be another room with a little solar system looking object. Behind it will be the last two Ore chests.
From the gate once again head left and you'll be at the room with two doors. Now with the Master Key you can head throught the right door and up at the end of the path will be the second Gate Medallion.
The third one is in the long corridor take the first door on the right down below. At the top of the room will be the last Gate Medallion.
The Chimes drop The Attendance/The Strange boss. And the Verglas Rune will drop after picking your "choice" (Make sure if you want ending D you do Nadia's quest before heading into the portal for your "choice")

There are three sets of two Haywards and one separate one at the beginning as you ascend The Dark Tower. They all drop an Ore so you can upgrade whatever you need to by heading back to the shrine below after killing them.

Ru'uk is first found at the river with the small bridge in (1-1). From the bridge head south down the river and at the waterfall he'll be waiting to meet you.
Once you've opened the gate in the first room of the Mausoleum (1-2) he'll be waiting at the top of the stairs to talk to you again.
He's last found at the legendary grave he's been talking about in the middle of the two paths for the Womb Keys in (1-3). He gives you a Doll Eye for being his friend. <3
Saipo is first found after you've turned on the fans and followed them up into the vents of The Brume Factory (2-2)
His parts are scattered around all over the factory. The first leg you'll find is on the left ledge, northwest end of the cafeteria.
The second part is in the small tower outside to the east. Head up the stairs and to the right, there will be a small room holding the shield.
His turret is past where he's located on the upper floor. Follow the catwalk heading back towards the main room. You'll find a small group of enemies and the part laying on the floor to the right.
Near the way top of the conveyor room by the Demon Key head left into the back pocket past the flame traps. A small room with enemies guards the other leg.
Head back and talk to Saipo to repair him and he'll meet you at the beginning of The Tower of Communion (2-3) afterwards.
Defeat the Vanguard head back down and talk to him again in the same spot and he'll move again to meet you before The Machine Mind to help you fight it.
Interacting with the Hayward armor at the end of the right path in (3-1) starts this quest.
At the end of the dungeon before the cells downstairs in 3-2 has the ghostly figure in the fetal position.
It'll move to where the floating enemies who like to gun you down along the long cliff side in (3-3) are. It'll give you a Doll Eye.
At the end of (4-1) is a tent leading to (4-2). To head in you'll need to talk to Yoruga who is sitting just to the right of the tent.
Talk to her once inside (4-2) she'll ask for wine. Directly to the left of the large tent is the slug man who will give you the wine. You can return to her sleeping on the floor. Head to the knife throwing show northwest to have the Doll wander off and get stuck in the crane machine. Play all the mini games around the area for the 5 silver coins.

• One from the man who wants to see the show he'll just give it to you. Near the bottom right
  
• The stand next to the free coin where you just break all the pots
  
• Blow the horns in any order northeast
  
• Use a mana attack from most weapons to ring the strength bell. Next to the crane games
  
• Defeat the warrior in the ring next to the knife throwing show

Talk to her once beating Dread King Milos. This ends her quest. No reward but needed for the best ending.
Nadia will first be sitting next to the shrine before the Pike Shrike in (5-1)
She'll then move to the secret elevator room on your way up the tower in (5-2)
In (5-3) the room past where you get the Master Key you'll go further past the Gate Medallion and head into the computer room and head to the other side to talk to her again.
Go defeat the boss, head to the portal and make your "choice", once you're back at the boss room. Nadia will be sitting on the floor to your left.
She'll move to the Metronexus sitting at the top of stairs.
Head back to (5-1) and she'll be waiting at the empty door directly forward as you head out. She'll cure you of your "choice"