Fallout 4 quests

General information
All quests are represented on the Pip-Boy 3000 Mk IV by a brief animation. Due to the Creation Engine, multiple quests can be marked active at the same time.

Act I

 * Out of Time
 * Jewel of the Commonwealth
 * Unlikely Valentine
 * Getting a Clue
 * Reunions

Act II

 * Dangerous Minds
 * The Glowing Sea
 * Hunter/Hunted
 * The Molecular Level
 * Institutionalized

Act III

 * Due to the structure of the game, progressing far enough into a faction quest line will result in turning other factions hostile.

Side quests
These 32 quests have no affiliation with any faction, nor are companion quests.
 * Cambridge Polymer Labs (quest)
 * Confidence Man
 * Dependency
 * Diamond City Blues
 * Emogene Takes a Lover
 * Here Kitty, Kitty
 * Here There Be Monsters
 * Hole in the Wall
 * Human Error
 * In Sheep's Clothing
 * Kid in a Fridge
 * Last Voyage of the U.S.S. Constitution
 * Mystery Meat
 * Order Up
 * Out in Left Field
 * Painting the Town
 * Pickman's Gift
 * Public Knowledge
 * Pull the Plug
 * Short Stories
 * Special Delivery
 * Story of the Century
 * The Big Dig
 * The Devil's Due
 * The Disappearing Act
 * The Gilded Grasshopper
 * The Marowski Heist
 * The Secret of Cabot House
 * The Silver Shroud (quest)
 * Trouble Brewin'
 * Vault 75
 * Vault 81

DLC quests
All quests require their respective DLC to be installed. and active.

Automatron

 * Mechanical Menace: The player answers a distress call, but arrives too late to save all but one member of the caravan: Ada. With robot workbench schematics in hand, the two confront the new threat.
 * A New Threat: Tracking down the mechanist begins with a trip to the General Atomics factory, pursuing a rogue signal.
 * Headhunting: The mystery can be cracked by retrieving Jezebel, one of the Mechanist's robobrains. The catch? She's held at the hangar beneath Fort Hagen satellite array, ripped apart by the Rust Devils.
 * Restoring Order: The player confronts the Mechanist in their lair beneath the RobCo sales and service center. The rewards include the Mechanist's armor and helmet.
 * Rogue Robot: Repeatable quest that involves cleaning up leftover Mechanist robots.

Far Harbor
 
 * Main
 * Far From Home
 * Forbidden Knowledge
 * Walk in the Park
 * Where You Belong
 * Best Left Forgotten
 * The Way Life Should Be
 * Cleansing the Land (Reformation)
 * Close to Home
 * Far Harbor
 * Living on the Edge
 * Blood Tide
 * Safe Passage
 * Hull Breach
 * Rite of Passage
 * The Hold Out
 * Turn Back the Fog
 * The Great Hunt
 * Acadia
 * Acadian Ideals
 * The Arrival
 * Hunting the Hunter
 * Data Recovery → The Price of Memory
 * The Nucleus
 * What Atom Requires
 * Visions in the Fog
 * The Heretic
 * The Trial of Brother Devin
 * Witch Hunt
 * Ablutions

Vault-Tec Workshop

 * Vault-Tec Calling: A mysterious signal leads the Survivor to a hidden Vault in the Commonwealth.
 * Better Living Underground: With the Vault uncovered, the challenge lies in gaining access inside.
 * A Model Citizen: The Survivor meets a pre-War Overseer and agrees to reactivate the Vault
 * Explore Vault 88: Many more surprises await in the depths of the caverns excavated for the purpose of expanding Vault 88.
 * Power to the People: The Overseer would like to test various experimental designs in practice. The power cycle is the first.
 * The Watering Hole: Then comes a fountain laced with mind-altering drugs.
 * Vision of the Future: And manipulating dwellers using eyesight diagnostic machines.
 * Lady Luck: And finally, the piece de resistance, a personal invention by Overseer Barstow, turning vice into something of use to the Vault.

Nuka-World
The following quests are tied to the main story, if the player accepts their position as Overboss  The following are repeatable quests available for the player as an Overboss The following quest allows a player to wipe out the raiders and secure Nuka-World again for the traders Finally, the following three quests are side quests
 * All Aboard
 * Taken for a Ride
 * An Ambitious Plan
 * The Grand Tour (Star Control  · High Noon at the Gulch  · Safari Adventure  · A World of Refreshment  · A Magical Kingdom)
 * Home Sweet Home (Claiming the Commonwealth)
 * Power Play (Cleaning House)
 * A Goods Defense
 * A Permanent Solution
 * Amoral Combat
 * Collaring Outside the Lines
 * Taking Out the Trash
 * Under the Collar
 * Capture Settlement/Clear Out Settlement → Subdue Settlement/Shake Down Settlement
 * Open Season
 * Cappy in the Haystack
 * Precious Medals
 * Trip to the Stars