The Molecular Level Main Story Quest
This quest will be triggered or can be aquired when you complete Hunter/Hunted quest.
Related points of interest
Stages of "The Molecular Level" quest
1. Have the Courser Chip Analyzed
I have the Courser Chip, but I don't know how to decode it. Doctor Amari knows a lot about Synth technology. I should ask her for help.
Speak with Doctor Amari, she will tell you that you have to ask for help the Railroad members.
The Railroad might be the only people with a way to decode the Courser Chip, but we're enemies. Maybe there's something in their headquarters I can use.
You have to complete Road to Freedom quest to get access to the Railroad HQ. Go there and talk to Desdemona. She will take you to Tinker Tom and he will decode the courser chip for you.
2. Return to Virgil
I have all the information I need from the Courser Chip. Now to go back to Virgil and figure out the next step in breaking into the Institute.
3. Get Help to Build the Signal Interceptor
The Signal Interceptor should get me inside the Institute, but I'll need help building it.
You can select only ONE faction to help you.
3.1. (Optional) Talk to the Brotherhood
Talk to Elder Maxson on The Prydwen. To be able to do this, you have to complete Shadow of Steel quest.
3.1.1. Talk to Proctor Ingram
3.1.2. Build the Reflector Platform
3.1.3. Talk to Proctor Ingram
3.1.7. Build the Console
3.1.8. Power up the Signal Interceptor
3.1.9. Talk to Elder Maxson
He will tell you about Doctor Li and it will start a new quest - From Within.
3.1.10. Use the Signal Interceptor
Step onto the platform, Proctor Ingram will give you a new quest - Outside the Wire.
3.1.11. Quest completed
The Signal Interceptor worked. I'm inside the Institute. Now to find Shaun.
3.2. (Optional) Talk to the Railroad
Talk to Desdemona in the Railroad HQ. You need to be a member of The Railroad, so you need to complete Tradecraft quest first.
3.2.2. Build the Reflector Platform
3.2.2.1. (Optional) Talk to PAM about Mercer Station
If you talk to her, you will receive a new quest - Mercer Safehouse.
3.2.3. Talk to Tinker Tom
3.2.4. (Optional) Search telecom sites for a Sensor Module
3.2.5. Build the Beam Emitter
3.2.6. Build the Relay Dish
3.2.7. Build the Console
3.2.8. Power up the Signal Interceptor
3.2.9. Talk to Desdemona
3.2.10. Use the Signal Interceptor
Step onto the platform, Desdemona will give you one more quest - Underground Undercover.
3.2.11. Quest completed
The Signal Interceptor worked. I'm inside the Institute. Now to find Shaun.
3.3. (Optional) Talk to the Minutemen
Talk to Preston Garvey in Sanctuary.
3.3.1. Talk to Sturges
3.3.2. Build the Reflector Platform
3.3.3. Talk to Sturges
3.3.4. (Optional) Search telecom sites for a Sensor Module
3.3.5. Build the Beam Emitter
3.3.6. Build the Relay Dish
3.3.7. Build the Console
3.3.9. Talk to Sturges
3.3.10. Use the Signal Interceptor
Step onto the platform, you will receive one more quest - Inside Job.
3.3.11. Quest completed
The Signal Interceptor worked. I'm inside the Institute. Now to find Shaun.
Next / new quests are From Within (Brotherhood of Steel), Inside Job (Main Story, Minutmen), Institutionalized (Main Story), Mercer Safehouse (The Railroad), Outside the Wire (Main Story, Brotherhood of Steel), Underground Undercover (Main Story, The Railroad).