The Molecular Level

The Molecular Level is a main story quest and achievement/trophy in Fallout 4.

Detailed walkthrough
At the end of The Glowing Sea, Virgil reveals that the Institute uses teleportation, and that this could be intercepted using information from a courser chip to construct a device, the Signal Interceptor. Before the Sole Survivor can utilize the newly acquired courser chip, it needs to be analyzed by someone familiar with the Institute's technology. The only person capable of doing this is Tinker Tom of the Railroad. If the Railroad has yet to be encountered, Dr. Amari will advise the player to follow the Freedom Trail to find the hidden Railroad HQ.

Once at Railroad HQ, speak to Desdemona and agree to her terms. Give the courser chip to Tinker Tom, who cracks the encryption and provides the code for the chip. If Tinker Tom is dead, there is a file on his terminal that automatically decrypts the data.

Return to Virgil. He offers the plans for the Signal Interceptor but now reminds the Sole Survivor of the favor that they promised him in their previous agreement: if the teleporter works, they must retrieve a serum from Virgil's old laboratory inside the Institute to cure his FEV affliction and make him human again. Accept his terms and receive the plans. However, the Signal Interceptor is no simple machine: expert help and a lot of resources are needed to construct it.

At this point, the Sole Survivor needs to make a choice to enlist the help of one of the three major factions (the Minutemen, the Brotherhood of Steel, or the Railroad). Speak to either Proctor Ingram (BoS), Sturges (Minutemen), or Tinker Tom (Railroad) and arrange for the construction of the teleporter. The chosen expert then travels to the building site and explains the requirements and necessary materials for each of the four components: the reflector platform, beam emitter, control console and relay dish.

The player can build the Signal Interceptor in the majority of allied settlements, including Boston Airport if they are allied to the Brotherhood. Note that both Home Plate and settlements from add-ons are excluded. Even though the Railroad suggests building it at Mercer Safehouse, one is not required to do so.

Constructing the Signal Interceptor
Build the stabilized reflector platform first in the target settlement, then speak to either Ingram, Sturges or Tom. Either of them gives the Sole Survivor the second list of resources required to complete the Signal Interceptor and will travel to (or spawn at) the settlement where it is built.

If building with the Brotherhood's help, Elder Maxson's permission is required before activating the Signal Interceptor. He moves from Boston Airport to the chosen settlement and might camp at allied settlements for the night along the way (he will be tagged on the Pip-Boy for his entire journey).

Requirements for the teleporter:
 * Enough flat surface area without any obstructions (the emitter needs to be built upon the platform, the combined structure - including a fusion generator to power it - can be squeezed in a 2x2x3 space).
 * Enough "size" allotment remaining at the settlement (the teleporter is quite large).
 * It requires 27 power.
 * The components have to be linked together with power cables on the same network.
 * For additional details regarding the construction of the Signal Interceptor, see its page.

When everything is built, linked together and supplied with enough power, the teleporter is ready for use. Talk to the expert and get ready for the voyage. The expert (of the assisting ally faction) instructs the Sole Survivor to stand on the platform, they are given a faction-dependent holotape, and then the teleportation process will commence.