Spoilers ahead! (obviously)

While a perfect achievement guide already exists, when doing a playthrough, I prefer something by chapter order, so I originally compiled this for myself and thought I'd share. If you find any errors, please let me know.

Aside from what I compiled from other guides, I've added counts for relevant achievements at the end of each chapter and a few extra notes.

Huge thanks and credit goes to the authors of the various guides I've compiled the information from:

• Perfect Achievement (SPOILERS) (COMPLETE) by Legendary
  
• Chest Guide by Bill Nye the [Redacted] Spy
  
• List of Books (Sky 3rd)[kiseki.wikia.com] from Kiseki Wiki

While I didn't directly pull any information from it, I want to mention The Legend of Heroes: Trails in the Sky the 3rd Walkthrough by Zoelius[gamefaqs.gamespot.com] which I used on occasion for guidance on my first playthrough. If you get stuck on anything, check out the walkthrough.

Difficulty level achievements are fairly self-explanatory. If you complete the game on Nightmare, you can get all of these in a single playthrough:

• Easy Peasy (Easy)
  
• Straight and Narrow (Normal)
  
• Proud Powerhouse (Hard)
  
• Only In Your Dreams (Nightmare)

EDITED (Nov 2020/2023): In Chapter 8, you will get a reward for running or not from battle. The problem here is that you only trigger the achievement when you get the reward. Thanks to Oguzhan for pointing out (in the comments) that you should be able get these in a single playthrough if you trigger "Fierce Fighter", reload to a previous point, flee from 300 battles, then trigger "Flightly Fighter".

Some commenters say that it's not much a grind if you stand still where a monster spawns and use the "turbo" option to fast forward and escape 300 times.

Personally, I would still find it quite a grind and normally do 2 playthroughs. So, if you also tend to do 2 playthroughs, choose one for your first playthrough and the other for your second playthrough.

• Flighty Fighter (Hidden): run from 300 or more battles
  
• Fierce Fighter (Hidden): never run from battle with at least 300 on record

Once you claim the reward, it doesn't matter if you run or not.

Aside from the difficulty level reward, these are only available in Nightmare mode:

• The Dadliest (Hidden): Defeat Cassius without choosing to make the fight easier if/when retrying.
  
• Farewell, My Nightmares (Hidden): Defeat Schwarzritter in the Farewell Arena.

In general, things should be listed in the most likely encounter order, so for the most part each chapter will have chests lists by area interrupted with information on doors.

The chapter sections cover the following achievements:

• Bookworm: 52 Books
  
• Starry-Eyed: 15 Star Doors
  
• Honeymoon: 6 Moon Doors (There are only 5 Moon Doors, but the Steam counter is 6.)
  
• Sunny Days: 5 Sun Doors
  
• Minigame Madness: 5 Minigames
  
• Sidetracked Chest-Tracker: 246 Chests before final chapter
  
• Please Erase My Memories (Hidden): Read a book you wish you hadn't, see Chapter 6
  
• You Know Too Much: "Who Wants to Be a Mirannaire?" on Maniac mode, see Chapter 6
  
• Tempting Fate: Defeat all Abyss fiends, see Chapter 8

Only the books in the Garden's Library counts, not the books near the Garden's Tree. I've included it in the guide but marked them optional.

Books do not have to be triggered in the same playthrough.
Thanks to @germicide1020 for the note in the comments.

For chests to count, make sure to open the chest and examine it again to get the chest phrase. There are more than 246 chests before the final chapter, so it's possible to get the achievement even if you miss some. Technically, what you need to do is trigger all the chest phrases, not the chests and you can trigger new ones from the same chests after a segment of day passes (h/t Bakahatsu in the comments), though it's easier to get it by getting a phrase for each chest so you don't have to backtrack. For more precise locations, see the original chest guide which has screenshots.

You will encounter many of the doors before you can open them. They are mentioned at the earliest time when you can open them rather than when you encounter them, but you should still trigger them when you first encounter them so that you can easily teleport back. Often, you will need to win a battle, minigame, etc. to get the reward.

Story based (hidden) achievements will be automatically received upon completion of each chapter:

• The Gralsritter (Prologue)
  
• Phantasma (Chapter 1)
  
• The Otherworldly Capital (Chapter 2)
  
• Golden Road, Silver Road (Chapter 3)
  
• The Dark Stigma (Chapter 4)
  
• Labyrinth of Shadows and Light (Chapter 5)
  
• The Guardians' Trials (Chapter 6)
  
• The Distant Flames (Chapter 7)
  
• The Future We Dream Of (Chapter 8)

Note: While the Carnelia books are available in the Library, reading it here will not count towards the achievement since it explicitly states the location. You will get another chance to read them in Chapter 2.

4 Chests

• 1x Teara Balm – 1st room
  
• 1x EP Charge – 3rd room
  
• 1x EP Charge – 5th room
  
• 1x Teara Balm - "

Chest Total: 4 / 246

8 Chests; Moon 1

• 1x Information – 1st area, straight ahead
  
• 1x Tear balm – 1st area
  
• 1x 300 mira – "
  
• Moon Door 1 (Part 1): Tita
  
• 1x Glam Chocker - warp area west of monument
  
• 1x Black Bangle – "
  
• 1x Extra Spicy Fries - warp area east of monument
  
• 1x Tear Balm – "
  
• 1x Smelling Salts – "

Chest Total: 12 / 246

5 Chests

• 1x Royal Spikes – Deck
  
• 1x Reviving Balm – Clinic
  
• 300 mira – Room next to Clinic
  
• Easy Paella (recipe) – Cafeteria
  
• 1x Hit 2 – Conference room

Chest Total: 17 / 246

4 Chests

• 1x Fresh Water - warp area south of monument
  
• 50x Earth, Water, Fire, Wind Sepith – "
  
• 1x Fishy Finaly - last area
  
• 50x Time, Space, Mirage Sepith – "

Chest Total: 21 / 246

• Star Door: 0 / 15
  
• Moon Door: 1 / 6
  
• Sun Door: 0 / 5
  
• Minigame: 0 / 5
  
• Book: 0 / 52

Hermit's Garden, Library area: Read all of Carnelia 1-10 + Finale

5 Chests

• 1x HP2 – 3rd floor orbal factory
  
• 1x Akashic Heart – Weapons shop, go through the door on the 2nd floor, then down the stairs
  
• 1x Smelling Salts – House next to weapons shop
  
• 1x Fried Phoenix – 2nd floor, Sunnybell Inn
  
• 1x Insulation Tape – House near the east side exit, 2nd floor

Chest Total: 26 / 246

5 Chests

• 50x Earth, Water, Fire, Wind Sepith – House near the exit to the south, 2nd floor
  
• 500 mira – Hotel 1st floor, upper left room
  
• 1x White Bracelet – Hotel 2nd floor, corridor
  
• 500 mira – Hotel 2nd floor, Upper right room
  
• 500 mira – Hotel 2nd floor, lower left room

Chest Total: 31 / 246

5 Chests

• 1x Proxy Puppet – Department store, right
  
• Septium Drops (recipe) – Department store, left
  
• 1x Softening Balm – Department store, top right corner
  
• 1x Bestia Coat – Imperial embassy, main office
  
• 1x Teara Balm – Imperial embassy, right back room

Chest Total: 36 / 246

Star Door 1: Grancel Castle: Julia and Mueller

9 Chests; Star 2

• 1x Black Bangle+ – Liberl News Service, 3rd floor
  
• 1x Swingwich – Coffee shop
  
• 1x Brain Roast – "
  
• 1x Teara Balm – House north of the coffee shop
  
• 1x S-Tablet - House notheast of coffee shop
  
• 50x Elemental Sepith – House to the right of the church, 2nd floor
  
• 1x Celestial Balm – Septian Church
  
• Star Door 2: Grancel Cathedral: Win 100+ battles.
  
• 1x Stun GB – Septian Church, lower left room
  
• 1x Teara Balm – Septian Church, lower right room

Chest Total: 45 / 246

8 Chests

• 1x Long Barrel 2 - Inside 1st warehouse
  
• 1x Teara Balm – 2nd area, southeast at the end of the narrow path
  
• 1x Crimson Eye – Slender path north of the previous chest
  
• 1x Purging Balm – Side of eastern warehouse
  
• 1x EP Charge – East, near the shipping containers
  
• 1x Teara Balm – Northeast corner
  
• 1x Scent - Northwest, behind the pillar
  
• 1x Purging Balm – Northwestern corner

Chest Total: 53 / 246

Sun Door 1: Jade Corridor: Josette; Minigame: Difficulty doesn't matter, so choose easy.

12 Chests

• 1x Shield 2 – Dinning room
  
• 1x Queenly Cookie (recipie) – Kitchen, 1st floor
  
• 1x Fluffy Crepe – "
  
• 1x Repellent Dish – Kitchen basement
  
• 1x Teara Balm – Kitchen basement
  
• 1x Teara Balm – 1st floor, left room
  
• 1x Pearl Earring – 2nd floor left corridor, last room
  
• 1x Glam Choker+ - 2nd floor, throne room
  
• 1x Zeram Powder – 2nd floor right halfway, 1st lower guest room
  
• 1x Attack 2 – Garden, south side
  
• 1x Teara Balm – Garden, west side
  
• 1x Haze – Queens room, 1st floor

Chest Total: 65 / 246

• Star Door: 2 / 15
  
• Moon Door: 1 / 6
  
• Sun Door: 1 / 5
  
• Minigame: 1 / 5
  
• Book: 11 / 52

Optional (not counted): Hermit's Garden, South of Tree: Read Liberl News (FC) 1-9 + Special

Star Door 3: Grancel Castle, Garden Terrace: Joshua and Kloe

14 Chests

• 1x Tearal Balm - Right path at the entrance
  
• 1x Sting Edges – Center north side
  
• 1x Silver Earring – Central west side
  
• 1x Amar Spiritus – "
  
• 100x All sepith – "
  
• 1x Kumo no tachi – Northwest
  
• 1000 Mira – "
  
• 100x All sepith – "
  
• 1x White Bracelet+ - Behind warp zone
  
• 1x Curia Balm – 2nd area, west square
  
• 1x Skull Pendant – 2nd area, west square
  
• 1x Aion Bow – Middle square
  
• 1x Gaia Greaves – East square
  
• 100x All sepith – East square

Chest Total: 79 / 246

14 Chests

• 1x Tearal Balm – Head left at the start
  
• 1x Gaia Greaves – East block
  
• 1x Hp 3 – Eastern square
  
• 1x Miso Fish – "
  
• 1x Castel Castella – "
  
• 1x Reviving Balm – Middle square
  
• 1x Tiger Heart – West
  
• 1x Stinger M – Northeast square
  
• 1x Skull Pendant – Behind warp zone
  
• 100x All sepith – 2nd area, west square
  
• 1x Attack 3 – 2nd area, west square
  
• 1x Silvahn – Middle square
  
• 1x Pearl Earring+ - East square
  
• 1x Reviving Balm – East square

Chest Total: 93 / 246

• Star Door: 3 / 15
  
• Moon Door: 1 / 6
  
• Sun Door: 1 / 5
  
• Minigame: 1 / 5
  
• Book: 21 / 52

Hermit's Garden, Library area: Read:

• Kitty-Talk for Dummies
  
• The Erbe Woodpecker
  
• Hertz's Adventure 1
  
• Hertz's Adventure 2
  
• 31 Cypress Trees

Sun Door 3 (Part 1): Grand Arena: Zin

Star Door 4: Golden Road: Zin

1 Chest

• Entrance Exam Results – Behind the teleporter in the regroup area

Chest Total: 94 / 246

Moon Door 3: Silver Road: Kloe and Entrance Exam Results

• Find classmates for the handouts:
  
  • Students in the classroom
    
  • Auditorium Backstage: Clara
    
  • Boy's Dormitory: Logic
    
  • Old Schoolhouse: Anton
    
  • Clubhouse: Lucy
    
  • Clubhouse Girl's Locker Room (must be last): Monika
• When Jill and Leo ask for help searching: Auditorium 2nd floor
  
• After receiving an envelope:
  
  • Clubhouse: Leo;
    
  • School: Dean;
    
  • leave the school
• As Jill in Boys' Dormitory: 2nd floor, 2nd door
  
• Searching:
  
  • Boys' Dormitory,
    
  • Auditorium backstage: talk to Jill,
    
  • (last) Clubhouse: Student Council's Room, examine the window and climb up.

4 Chests

• 1x Mind 4 - north room by the stairs
  
• 1x Luck (Fortune) - north room end of hallway
  
• Freezing Meatballs (recipe) - south room by the stairs
  
• 1x Carnelia Bracelet - south middle room

Chest Total: 98 / 246

15 Chests
** are Hidden chests. Ensure you try all the switches in both directions when applicable.

• 1x Heat-Resistant Boots – East Door Area, Middle
  
• 1x **Skull Pendant+ - in the lava
  
• 1x Reviving Balm – East Door Area, Eastern area
  
• 1x **Heat-Resistant Boots – "
  
• 1x EP Charge – "
  
• 1x **Heat-Resistant Boots – 1st area, west
  
• 1x UF Pie – 1st area near the northern door
  
• 1x **Heat-Resistant Boots - North Door Area, East
  
• 1x Fragrant Juice - North Door Area, Southwest
  
• 1x **Dragon Tree Jumpsuit – North Door Area, Middle
  
• 1x Attack 4 – North Door Area, Central area on lava
  
• 1x Feather Brooch – North Door Area, Northwestern corner on lava
  
• 1x **Kaiser Knuckles – North Door Area, Northwest
  
• 1x EP Charge – "
  
• 1x Crimson Eye – Behind boss area

Chest Total: 113 / 246

Star Door 5: Balstar Channel: Anelace

12 Chests

• 1x Lily Necklace – 1st area after entrance, southwest
  
• 1x Triplet Ice – 1st area, inside the river to the south
  
• 1x Celestial Balm – 1st area, inside the river to the north
  
• 1x HP 4 – 1st area, Northeast
  
• 1x Curia Balm – 2nd area, North
  
• Sludgy Cookie (recipe) – "
  
• 1x Calvary Cross – 2nd area, East dead-end
  
• 1x Tearal Balm – 3rd area, middle
  
• x100 Earth, Water, Fire, Wind Sepith – 3rd area, middle behind some trees
  
• 1x Gatling Gear – 3rd area, northwest
  
• 1x EP Cut 4 – "
  
• 1x Kidney Daggers – 4th area, northeast

Chest Total: 125 / 246

Moon Door 2: Grancel Branch: Schera

• Sewers East: 5 chests
  
• Sewers West: 2 chests

Chest Total: 132 / 246

10 Chests

• 1x Spiral Grill – 1st floor, first room when entering
  
• 1x Tearal Balm – 1st floor
  
• ID Card – 1st floor, Room behind the bulkhead
  
• 1x Juggernaut – 2nd floor, 1st room on left
  
• 1x Zeram Powder – 2nd floor, center (bridge set to green)
  
• ID Card 2 – 2nd floor, west (bridge set to green)
  
• 1x Night Goggles – 3rd floor, 1st room to the right in the 1st dark area
  
• 1x Curia Balm – 3rd floor, room to the east in the 2nd dark area
  
• 1x Moonglasses – 3rd floor, room to the south in the 2nd dark area
  
• 1x Silver Earring+ - 4th floor

Chest Total: 142 / 246

Star Door 6: Grimsel Fortress: 20+ recipes. Tip: Eat items to learn its recipe.

• 11 chests

Chest Total: 153 / 246

Moon Door 1 (Part 2): Jade Corridor: Tita And Agate. Head to the roof of ZCF.

• Star Door: 6 / 15
  
• Moon Door: 4 / 6
  
• Sun Door: 2 / 5
  
• Minigame: 2 / 5
  
• Book: 16 / 52

Hermit's Garden, Library area: Read: Gambler Jack 1-13 + Finale

Sun Door 2: Fisherman's Guild: Estelle. Tip: Use small fish to catch big ones, especially as bait with the Metal Rod Trident.

Moon Door 4: Saint-Crox Forest: Estelle and Joshua

8 Chests; Star 7

• 1x Feather Brooch+ - 1st area, middle
  
• 1x EP Charge II – 1st area, northeast
  
• Star Door 7: Labyrinth of Light: No requirement. Tip: Be immune to Petrify.
  
• 1x Lighter – 1st area, northwest
  
• 1x Ugetsu Zanshin – 2nd area, southwest
  
• 200x All Sepith – 2nd area, middle
  
• 1x Phantom S – 2nd area, circle southwest to the monument
  
• 1x Mirage Ring – 2nd area, take the warp west of the monument
  
• 1x Long Barrel 3 – 2nd area, take the warp east of the monument

Chest Total: 161 / 246

9 Chests; Sun 4

• 200x All Sepith – Right at the first crossroad
  
• 1x Crest Charm – Bottom path at the first crossroad
  
• 1x Celestial Balm – After taking the warp, east of the large circle
  
• 1x Lily Necklace+ - North of the previous chest
  
• 1x Destiny Card – next warp area, chest is located east of the map at a dead end
  
• Sun Door 4: Umbral Labyrinth: Destiny Card
  
• 1x Apeiron – Dead end west of previous chest
  
• 1x Moonglasses+ - Before the warp point
  
• 1x Strega-0 – Inverted Y branch to the southwest
  
• 1x Springed Egg – Before the monument, west of the map at a dead end

Chest Total: 170 / 246

5 Chests; Star 8

• 1x Celestial Balm – 1st area
  
• Star Door 8: Luminous Labyrinth 2: Olivert and Mueller
  
• 1x Amberl Bracelet – Southeast warp
  
• 1x Giardino – 3rd area, west
  
• 3,000 mira – 3rd area, west
  
• 200x All Sepith – Top of spiral staircase

Chest Total: 175 / 246

Star Door: 8 / 15
Moon Door: 5 / 6
Sun Door: 4 / 5
Minigame: 4 / 5
Book: 30 / 52

Hermit's Garden, Library area:

• Don't have Schera in your party, speak to her, then read the talked about book on the shelf. Unlocks Please Erase My Memories.
  
• Doll Knight 1-21 + Finale. Unlocks Bookworm.

3 Chests

• 1x Silver Gem – Northeast of the road in 1st area
  
• 1x Sapphire Gem – North of 1st area, Southeast
  
• 1x Ruby Gem – East of 2nd area, near the middle

Chest Total: 178 / 246

15 Chests; Moon 5

• 10,000 mira – Schoolyard, northwest
  
• Star Door 9: Jenis Royal Academy - Girls' Dormitory: 50,000 Mira.
  
• 1x Fish Skewers – Girls’ Dormitory, 1st floor room to the left
  
• 1x Mute 2 – Schoolyard, Northeast corner
  
• 1x Sigrdrifa – Auditorium, left of stage
  
• 1x Tornado Fan – Main Building, 1st floor, Faculty Lounge
  
• 1x Zeram Capsule – Main Building 2nd floor, Natural Sciences Classroom
  
• 10,000 mira – Clubhouse 1st floor
  
• 1x Gargan Armor – Clubhouse 2nd floor, Student Council Room
  
• 10,000 mira – Schoolyard, southwest
  
• 10,000 mira - "
  
• 1x Tomato Fondue – Boys’ Dormitory, 1st floor room to the left
  
• 1x Zeram Capsule – Old Schoolhouse, left side (outside)
  
• 1x Punisher – Go outside from the room in the back of the 1st floor
  
• 1x T-Anklet – 2nd floor right side
  
• Moon Door 5: Jenis Royal Academy, Old Schoolhouse: Luck (Fortune) Quartz. Unlocks Honeymoon.
  
• 200x All Sepith – 2nd floor left side, 1st room

Chest Total: 193 / 246

19 Chests; Star 10; Sun 3 (Part 2; optional)

Note: ** are not chests, so don't count towards total

• **1000x All Sepith – 1st floor, conveyor room, right conveyor belt
  
• 1x Mumei Jittetsu – 1st floor, conveyor room, back left
  
• 1x Poison 2 – 1st floor, southeast in small room
  
• 1x Gold Crests – 1st floor, southwest room
  
• 1x Cased-in-Jelly - "
  
• 1x Napalm Meat - "
  
• 1x Ingenuity – 1st floor, northwest room
  
• 1x Zeram Capsule – 2nd floor, first room to the left
  
• **1000x All Sepith – 2nd floor, southwest room, inspect the open capsule
  
• 1x Mirage Gem – 2nd floor, room located west in the container room
  
• 1x Confuse 2 – 2nd floor, room before container room (green cardkey)
  
• Star Door 10: Looking Glass, 2nd Floor, Green Cardkey: Renne
  
• 1x Water Gem – 3rd floor, southwest room
  
• **1000x All Sepith – 3rd floor, southwest, blue orb that is outside
  
• 1x Tasty Medicine – 3rd floor, hanger
  
• 1x Tear All Balm – 3rd floor, big room, chest is in the southwest corner
  
• 1x Grand Slam – 3rd floor, northeast room (blue cardkey)
  
• Tournament Invitation - "
  
• Optional: Sun Door 3 (Part 2): Grand Arena: Tournament Invitation.
  
• 1x Celestial Balm - "
  
• 1x Celestial Balm – 2nd floor, room located east in the container room (blue keycard)
  
• 1x Wood Gem – 2nd floor, east door in elevator room (blue keycard)
  
• 1x Sleep 2 - 1st floor, hanger (red keycard)
  
• 1x Gargan Armor – 1st floor, small room in west corridor (green keycard)

Chest Total: 212 / 246

Star Door 11: Looking Glass, 1st Floor, Blue Keycard: Win battle.

Optional (not counted): Hermit's Garden, South of Tree:

• The Hundred Days War
  
• Ruan Economics 1-3
  
• Septium Optic Annals

34 Chests; Star 12

• 1x Zeram Capsule – Soldat Army Road, behind the warp point
  
• 1x Master Beads – Courtyard
  
• 1x Tear All Balm – 1st floor barracks, first room to the east
  
• Trap Chest: B-01 Key – 1st floor barracks, last room to the east
  
• 1x Force Flag – 1st floor barracks, room to the west
  
• 1x Topaz Gem – Command, Dungeons
  
• 1x EP Charge III – "
  
• 1x Fruity Temptation – "
  
• C-01 Key – "
  
• 1x Amazing & Sparkling – 1st floor Command, small room in east hallway
  
• 1x Curia Balm – 1st floor Command, small room in east hallway
  
• 1x Blind 2 - 1st floor Command, small room in east hallway
  
• Star Door 12: Impregnable Fortress, Command: Richard.
  
• 1x Zeram Powder – 1st floor Command, upper door after using C-01 key, then take the left door
  
• 1x Tearal Balm – Room next to previous chest
  
• 1x Wind Gem – 1st floor Command, left after using C-01 key, bottom door
  
• 1x Long Barrel 3 – 1st floor Command, section below the previous chest
  
• 1x EP Charge III – 2nd floor Command, 1st door encountered
  
• 200x All Sepith – 2nd floor Command, small room to the east
  
• 1x Celestial Balm - "
  
• C-02 Key – 2nd floor Command, small room to the south
  
• 200x All Sepith – 2nd floor Command, northeast
  
• 1x Crest Charm+ - "
  
• 1x Curia Balm - "
  
• 1x S-Tablet – 2nd floor Command, southwest of stone monument
  
• 1x Celestial Balm – 3rd floor Command, small room to the south
  
• 1x Zeram Powder – 3rd floor Command, room below previous chest
  
• 1x Onyx Gem - 3rd floor Command, small room to the southeast
  
• 200x All Sepith – 3rd floor Command, east
  
• 1x Tear All Balm – 3rd floor Command, small room in the northeast
  
• 1x Yin-Yang – 3rd floor Command, small room north of previous chest
  
• C-03 Key – 3rd floor Command, from previous chest, follow door at the end of the hallway
  
• 1x Curia Balm – 3rd floor Command, small room before the monument
  
• 1x Super Gladiator Headband - Landing Port, east
  
• 1x Super Gladiator Belt - Landing Port, north

Chest Total: 246 / 246; Unlocks Sidetracked Chest-Tracker.

44 Chests; Star 13; Sun 5

• 1x Celestial Balm – Stern 1F, 2nd door, east side of the central aisle
  
• 1x Gargan Armor - "
  
• 1x Insulation Tape - "
  
• 1x S-Tablet – Stern 1F, 3rd door, west side of the central aisle
  
• 200x All Sepith - "
  
• 1x Zeram Capsule - "
  
• 1x Celestial Balm – Stern 1F, 4th door, east side of the central aisle
  
• 200x All Sepith - "
  
• 1x Gladiator Belt - "
  
• 1x EP Charge III - "
  
• 1x Crab Special - "
  
• 1x Tear All Balm - "
  
• 1x Olibanum Ray – 2nd floor, small room to the east
  
• 1x S-Tablet – 2nd floor, small room to the west
  
• Star Door 13: The Black Ark, Stern 2F: Win 400+ battles.
  
• 1x Emerald Gem – Stern 2F, 2nd floor, small room to the east
  
• 1x Lebensborn – Stern 2F, 2nd floor, small room to the west
  
• 1x Insulating Tape – Stern 2F, 1st floor, east side of the central aisle
  
• 1x Curia Balm - "
  
• 1x Gold Gem - "
  
• 1x Lighter+ - "
  
• 1x Celestial Balm - "
  
• 1x EP Charge II - "
  
• 1x Tear All Balm – Room slightly north of the previous one
  
• 1x Bloody Slaughter - "
  
• 1x EP Charge II - "
  
• 1x Gladiator Headband - "
  
• 1x Tear All Balm - "
  
• 1x Curia Balm - "
  
• 5,000 mira – Holding Cells, cell #2
  
• 1x Seal 2 – Holding Cells, cell #4
  
• 1x Strike 2 – Forecastle 1F, 2nd floor, small room to the west
  
• 200x All Sepith – Forecastle 1F, 2nd floor, small room to the east
  
• 1x Emergency Puppet - "
  
• 1x Curia Balm - "
  
• 1x Reviving Balm – Forecastle 1F, east side of central aisle
  
• 1x Cloak - "
  
• 200x All Sepith - "
  
• 5,000 mira – Forecastle 1F, room across previous one
  
• 1x Super Gladiator Belt - "
  
• 1x Heaven’s Eye - "
  
• Sun Door 5: The Black Ark, The Forecastle 1F: In inventory, have all level 5 quartz (that you can make, not including rewards/chests). Unlocks Sunny Days.
  
  • Beat minigame on Normal mode: Unlocks Minigame Madness.
    
  • Beat minigame on Maniac mode: Unlocks You Know Too Much.
• 200x All Sepith – Forecastle 2F, 3rd room, east side
  
• 5,000 mira – Forecastle 2F, 4th room, east side
  
• 200x All Sepith – Forecastle 2F, 2nd room, west side
  
• 1x Freeze 2 – Forecastle 2F, 4th room, west side

Chest Total: 290 / 246

Star Door: 13 / 15
Moon Door: 6 / 6
Sun Door: 5 / 5
Minigame: 5 / 5
Book: 52 / 52

17 Chests

• 1x Celestial Balm – 2nd area, southeast
  
• 1x Tabernaculum – 2nd area, northeast
  
• 1x EP Charge III – 2nd area, northwest
  
• 1x Cosmic Gear – 2nd area, southwest
  
• 1x Vajra – 3rd area, middle
  
• 1x Beastly Stew – 3rd area, northeast
  
• 1x Wobbly Rainbow – 4th area, south
  
• 1x Blood Extract – 4th area, west
  
• 1x Shine Sphere – 4th area, middle
  
• 1x Tear All Balm – 5th area, middle
  
• 1x Purgatorio - "
  
• 1x Dragon Boots - "
  
• 1x EP Charge III - "
  
• 1x Sapphirl Necklace – 5th area, northwest
  
• 1x Grail Locket – 6th area, northwest
  
• 1x Celestial Balm – 6th area, northeast
  
• 1x Tear All Balm – 7th area, north near the exit

Chest Total: 307 / 246

• Star Door: 13 / 15
  
• Moon Door: 6 / 6
  
• Sun Door: 5 / 5
  
• Minigame: 5 / 5
  
• Book: 52 / 52

Note: Since chests in the final chapter don't count, I haven't listed them here. Though there are 16 chests in the Abyss Dungeon and 73 chests in Phantasmagoria. Check the Chest Guide for more information.

Optional (not counted): Hermit's Garden, South of Tree:

• Liberl News (the 3rd) Special Issue
  
• Liberl News (SC) 1-11

Note: If you've read everything up to this point, you get a really nice accessory.

Hermit's Garden, Fountain: Get a quartz for fleeing or not from 300+ battles: Unlocks Flighty Fighter or Fierce Fighter.

Fight all 4 bosses in a row without leaving the dungeon: Unlocks Tempting Fate.

• Star Door 15: The Abyss, Depths: Renne
  
• Optional: Sun Door 3 (Part 3): Grand Arena: Tournament Invitation (from Abyss 4 B17, south).
  
• Star Door 14: The Black Ark, Sanctuary: Complete all the other doors. Unlocks Starry-Eyed.

• Star Door: 15 / 15
  
• Moon Door: 6 / 6
  
• Sun Door: 5 / 5
  
• Minigame: 5 / 5
  
• Book: 52 / 52

That's it. Thanks for reading!