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Fallout 4: The Molecular Level quest walkthrough

How to complete The Molecular Level quest in Fallout 4.

A robot stands in front of a city in Fallout 4
Image credit: Bethesda Softworks

The Molecular Level is the ninth main quest in Fallout 4, leading to the events that will culminate in the end of Act Two. It begins straight after you complete Hunter/Hunted, and will set you on the path toward the Institute.

You'll also need to enlist the help of one of the game's three Factions to help complete it. These factions include The Minutemen, the Brotherhood of Steel, and the Railroad. Choosing which one to side with will have important implications for the end of Fallout 4, so you'll need to choose carefully. In our The Molecular Level walkthrough for Fallout 4, we sided with the Railroad, so bear that in mind as you follow along.

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The Molecular Level walkthrough for Fallout 4

Once you've materialised back in Goodneighbor, make your way along the alley to the left of the gun store and return to the Memory Den. Doctor Amari can analyse your newly-acquired Courser Chip, so locate her onstage and initiate conversation. Once she asks you about your adventures in The Glowing Sea, reveal that you managed to get help from Virgil.

Amari explains that she doesn't know how to crack the Courser chip, but points you in the direction of a group that can help. Ask about the organisation and you'll receive a code phrase - “Follow the Freedom Trail”. See what else you can learn about the Freedom Trail and the mysterious Railroad Faction, then promise Amari that you'll track them down.

Find the Railroad

You might recall that we had a fleeting brush with the Freedom Trail earlier in the game - courtesy of the robot tour guide on Boston Common, near Park Street Station. The Road to Freedom quest has been sat in your Pip-Boy log ever since - and it's finally time to take care of it. When you're ready to continue, exit the Memory Den, bring up your Pip-Boy map and fast travel straight to Boston Common.

When you reach your destination, head along the road to the north, dealing with any hostiles in the area. Keep Boston Common to your left and, a short way on, you'll spy a fountain and the Tour Bot nearby.

If you haven't already, approach the Tour Bot and engage him in conversation. Ask the robot about the Freedom Trail and you'll be told to follow the red path through the city's streets. When the Tour Bot is done, turn your attention to the fountain and locate the sign reading. “At Journey's End, follow Freedom's Lantern”.

Follow the Freedom Trail

Immediately below the sign, you'll spot a Freedom Trail marker. Examine it then look for the red line on the ground, leading away from Boston Common. Follow the line out of the park and stay close as it moves north along the road.

Up ahead, the line passes around Park Street Station and turns north-west. Shortly, it crosses over the road, leading you toward Massachusetts State House. Examine the next marker on the ground then continue tracking the line as it moves back across the road.

Almost immediately, the line disappears beneath an abandoned car then swings back toward Park Street Station, this time on the right-hand side of the road. Follow the line as it turns north and deal with any hostiles that you encounter on the way. Be sure to examine the marker hidden behind the bus on the right before continuing.

Keep pushing forward until you near the foot of the tall red tower then take a right. Up ahead, you'll spot the sign pointing toward Goodneighbor from earlier in the game.

As the line crosses the road to the right, you'll spot another marker - examine it to get the next piece of the code. When you're ready to continue, turn left at the junction and follow the road north, keeping an eye out for mongrels (including an alpha variant) as you go. Climb the slope ahead and drop off the end, taking out the ghouls to the right when you land. Note that killing and looting the Legendary Feral Ghoul Stalker will earn you the Never Ending Pipe Pistol - able to hold an unlimited amount of ammo.

Immediately to the right on the ground, you'll spy another marker. Examine it then follow the line as it swings around to the east. Climb the steps ahead and prepare to deal with another round of ghouls. When it's safe to proceed, resume your journey east and descend the steps.

Fend off the Super Mutants

Be careful as you enter the next area - there's a super mutant and mutant hound roaming ground level and a missile-launching super mutant stationed on the raised platform to the left of the brown building.

As you near the right-hand side of Faneuil Hall, you'll be ambushed by several more super mutants. One of these is a Super Mutant Suicider, who'll attempt to run at you and detonate a mini nuclear bomb. Quickly put some distance between you and your target and use VATS to target his carrying arm. When he's down, eliminate the remaining hostiles in the area then examine the marker on the line by the statue. Finally, follow the line as it moves along the right-hand side of the building.

Take a left at the end of the alley and continue tracking the line as it moves north. A little way ahead, it crosses the road and starts travelling east. Stay with it as it swings around to the north again then examine the marker ahead. Note that there are more super mutants and mutant hounds in the area - so get ready for another fight.

Once the street is clear, push forward and stay close to the line as it turns west. Work your way around the statue ahead and examine the final marker just beyond it.

Enter the Old North Church

This marks the end of the trail, leaving you with the following marker clues (arranged in numerical order): 1 - R, 2 - A, 3 - I, 4 - L, 5 - R, 6 - O, 7 - A, 8 - D.

Looks like you're in the right place - so enter the Old North Church ahead to continue.

Inside the church, pass through the hole in the wall and enter the large, ghoul-filled chamber. Clear the area of hostiles and locate the door to the right of your entrance hole. Head on through the door, raid the First Aid kit to the left and descend the steps at the end of the passage. Take a right at the bottom and follow the tunnel around to the west.

Eliminate the ghoul that attacks then take a right at the end of the passage. Continue north, dealing with one last ghoul, and locate the Freedom Trail Ring on the wall to the right.

Your next task is to spin the ring clockwise and counter clockwise, spelling the codeword 'RAILROAD' that we gathered along the Freedom Trail. Line each letter up with the arrow and press the central button after each one to open the secret door.

Slip through the door and descend the steps at the end of the passage. When the woman ahead begins to speak, draw in closer until the dialogue options appear. Explain that you're not her enemy and that Doctor Amari sent you. Next, tell her your story.

When Desdemona finally introduces herself, ask to hear more about the Railroad. This will bring the 'Find the Railroad' portion of the current quest (plus the 'Search for the Railroad' portion of the Road to Freedom quest) to a close.

Talk with Desdemona

Climb the steps to the east and follow Desdemona along the passage. Head through the door at the end to access Railroad HQ. On the other side, descend the steps and approach Desdemona to the right. When she informs you that the group will help, provided that you give them the Courser Chip, ask what they want it for. Tell Desdemona that she can take the chip then approach Tinker Tom at the nearby desk.

Wait for him to work his magic then, once the analysis is complete, prepare to return to Virgil in The Glowing Sea.

Return to Virgil

Equip your hazmat suit then retrace your steps through the church until you're back outside. Next, call up your Pip-Boy map and fast travel to the Rocky Cave in the far south-west.

On arrival, enter the cave to reach Virgil's laboratory. Follow the passage along and speak with Virgil. Tell him that you have the code and reveal that the Railroad helped you to crack it. As Virgil explains, you'll need to hijack the Institute's teleportation signal to make your way inside. Reassure him that his science skills are up to the task then tell him that you've got the device covered.

Get help to build the signal

Once the conversation is over, you're going to need find some help in order to build Virgil's device. As such, three optional objectives have been added to your log:

  • Talk to the Railroad
  • Talk to the Minutemen
  • Talk to the Brotherhood

In order to complete the current quest, you'll need to align yourself with one of these factions and work your way through their introductory quest if you haven't done so already.

For the purposes of this guide, we'll be joining forces with the Railroad - but you could also deal with the Minutemen or the Brotherhood if you prefer.

Talk to the Railroad

When you're ready to discuss Virgil's device with the Railroad, exit the cave and fast travel back to Old North Church. Enter the building and wind your way down through the crypt to reach Desdemona. Engage her in conversation and confirm that you know about synths. Tell her to go on and assure her that you'd risk your life for a synth. Finally, end the conversation to complete Road to Freedom and to add Tradecraft to your quest log.

Note that approaching Desdemona again will let you discuss Virgil's schematic. She'll agree to help provided that you assist Deacon with his task first.

- Keep reading for our guide to completing Fallout 4: Tradecraft, the next quest in the game.

- Head back to the first page for the rest of our Fallout 4 guide.

You can also read our guides on where to find all of Fallout 4's Bobblehead locations, how to locate and romance all Fallout 4 companions, how to use cheat and console commands to help you out in combat, and how to get started with Fallout 4's base building.

Plus, we've also got a Fallout 4: Far Harbor walkthrough if you're looking for how to complete Fallout 4's main expansion.