The Molecular Level

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

Synopsis
With a courser chip at hand, the Sole Survivor will need to find The Railroad and get their help with using the chip in order to successfully infiltrate the Institute.

Walkthrough

 * 1) With the courser chip in hand, the Sole Survivor will need to travel back to Memory Den in an attempt to utilize the chip. As she does not have the proper equipment, she will refer the Sole Survivor to The Railroad, as an alternative method, in which they will need to follow the Freedom Trail in order to gain access to the Railroad HQ, should they have not done so already.
 * 2) After locating the Railroad HQ and speaking with the faction's leader, Desdemona, she will send the Sole Survivor to Tinker Tom in order to have the courser chip properly analyzed.
 * 3) Tinker Tom will need specialized plans in order to build a teleporter device, which leads the Sole Survivor traveling back to Virgil in order to obtain such plans.

Building the teleporter device
At this point, the Sole Survivor will have numerous options in regards to building the teleporter device necessary to infiltrate the Institute with, and this choice will greatly affect their actions further into the quest line.

Brotherhood of Steel:
 * 1) Should the Sole Survivor choose the Brotherhood of Steel, they will need to gain the trust and respect of Paladin Danse by progressing through his short quest line, which can be achieved by first helping his recon team repel an attacking horde of feral ghouls at the Cambridge police department.
 * 2) After becoming an initiate within the BoS ranks, permission from Danse will need to be obtained in order to use BoS resourced to build the signal interceptor with.
 * 3) With permission obtained, the Sole Survivor must then speak with the BoS scientists aboard the Prydwen, progressing through Elder Maxson's introductory quest, which will see to Proctor Ingram moving off-ship to the airport base.
 * 4) Meeting Ingram at the airport base, she will give the Sole Survivor access to a small portion of the base that can be used as a settlement of sorts, and she will help out with the supplies needed.

Minutemen:
 * 1) After helping Preston Garvey and his group find a new home, whether at Sanctuary Hills or somewhere else, the Minutemen will become an option for aid in the building of a signal interceptor.
 * 2) Preston will request that the Sole Survivor help out with some of the local settlements, first, and afterwards, he will allow for the Sole Survivor to request help from the local engineer, Sturges.
 * 3) Sturges will then help out with the interceptor's construction, by handing over some basic supplies, and giving a few clues as to what to build and where.

The Railroad:
 * 1) Return to Old North Church after speaking with Virgil again, and hand the plans over to Desdemona. She will express her gratitude, and will request for the Sole Survivor to prove their worth and dedication towards the faction's causes, by helping Deacon reclaim their old headquarters at the Switchboard, which is currently overrun by a large group of synths.
 * 2) After returning to the Railroad HQ alive, and either lying to Desdemona with Deacon about what all happened on the mission, or telling the full truth, she will give the Sole Survivor permission to obtain help building the interceptor from Tinker Tom.

Misanthropic Moxie:
 * 1) So long as the Sole Survivor has access to a settlement's workbench, they may build the signal interceptor themselves at said settlements, without the aid of any major factions. This will require collecting more resources than normal demand, but is still easily possible.

Conclusion
Once the teleporter and signal interceptor have been built, and they have been connected properly to their power sources and command console, the teleporter can finally be utilized, either by the Sole Survivor or a faction scientist/engineer, which will send them straight into the heart of the Institute.