Fallout 4: The Molecular Level - Find the Railroad, Road to Freedom, Build and Power up the Signal Interceptor
Once you get back to the Goodneighbor, first head towards the gun store and return to the Memory Den. Let Doctor Amari analyze the Courser Chip you acquired and also inform her that you got he help from Virgil in your Glowing Sea Adventure. Amari then informs you about the failure to crack this Chip and also asks you to have few words with others who can crack this code.
Find the Railroad
Go ahead and talk to few group and they will give you a phrase 'Follow the Freedom the Tail' and get on track to find and track them down. You can check your Pip-Boy to located and mark the Freedom Tail and fast travel to Boston Common to continue the quest.
As you reach Common Boston and head north until you come across a fountain and a Tour Bot nearby, but be careful as you move you'll be attacked by few hostiles. Now to and interact with the Tour Bot and ask him about the Freedom Tail. He will soon ask you to follow the red path until you locate the sign reading 'At Journey's End' now follow the Freedom's Lantern.
Now keep examining the trail marker and look the path leading towards the Boston Common. Keep following the marker and you discover Massachusetts State House, continue moving and you'll see a line getting disappeared beneath a car. Make sure you check the marker behind the Bus on the right.
You must have discovered Old Granary Burying Ground so continue heading to the next marker and get the next piece of code, as you move forward you'll come across Legendary Feral Ghoul Stalker and if you loot him then you'll be rewarded a Never Ending Pipe Pistol which has unlimited ammo. In Old Corner Bookstore, you will be haunted by few Super Mutant in the building. Moving forward in Faneuil Hall bunch of Super Mutant Suicider which will detonate a mini nuclear bomb so play safe.
Once you've reached the Old North Church safely, this means you have made it till the end of the tail nad now you need to arrange the marker clues in numerical order like: 1 - R, 2 - A, 3 - I, 4 - L, 5 - R, 6 - O, 7 - A, 8 - D which makes you enter the Old North Church in search of the Railroad. Inside the church goes and pass through the hole in the wall, then eliminate all the Ghoul that attacks you.
Talk to Desdemona
As head down the steps to the end of the Passage, you will hear a woman begins to speak and you will have the option to explain to her why you are here and who have sent you. Then Desdemona will introduce herself and tell you more about the Railroad and end of the current quest Search for the Railroad and Road to Freedom. now Climb the steps and follow Desdemona to the door at the end to access the Railroad HQ. Later she will inform you about the group which will provide information about the Courser Chip and then approach Tinker Tom at the nearby desk. Once he finishes his work it's time return to Virgil in the Glowing Sea.
Return to Virgil
To return to Virgil, you need to re-equip the hazmat suit and fast travel to Rocky Cave. Enter the Cave and locate Virgil's Lab by following the passage and then inform him about the code you have received from the Railroad. Now Virgil will ask you to hack the Institute's teleportation signal to get inside safely. After the conversation is over you will have three optional objectives added to your log.
Get Help to Build the Signal
In order to get some help to build the Teleporter, you need to complete one of the faction and get the scientist available. Whichever faction you choose, you need to complete at least 2 side quest of them to get the things working. Or you can also build the Teleporter Signal by yourself, Virgil will give you the plans to build the device.
Sooner or later you'll need to build the device in order to continue with the Main Story quest. The Building of the Transporter requires several materials and when ready the Main Quest: The Molecular Level comes to an end and new Mission will be added to you Log.