Heh. Haven't you been paying attention? You don't find the Institute. The Institute finds you. You open the closet, it's just a closet. You can never find the monster that hides inside. Not until it jumps out at you.But I think we've been talking long enough. We both know how this has to end. So... you ready?
Without Dogmeat fresh on Kellogg's trail, the Sole Survivor will need to track down the kidnapper, but not before overcoming a few obstacles.
As soon as Dogmeat is given Kellogg's scent from the still smoldering cigar, he will immediately lead the Sole Survivor back out of Diamond City, where he will begin heading towards a small pond to the southwest. On a ruined deck near this pond, yet another smoldering cigar will be found, which will need to be given to Dogmeat in order to pick up a more fresh trail.
Dogmeat will then lead the Sole Survivor to some nearby railroad tracks, and once reaching the freeway underpass, the party will need to deal with a group of wild dogs in order to pick up some bandaging that contains a trace amount of Kellogg's blood, leftover from a recent hostile encounter.
The scent from the blood will lead the party to a metal shack on the same railroad from earlier, which has been heavily booby trapped by an unknown wastelander, which must be traversed in order to discover a bottle of Kellogg's Gwinnett ale.
Sniffing the ale, Dogmeat will renew his search, which leads to the party crossing a bridge leading into a decrepit town infested with feral ghouls.
After fighting off or sneaking around the feral ghouls, the party will discover a crippled assaultron near the town's exit, which must be spoken to, in which it will then power down permanently.
Continuing onward, the party will discover Fort Hagen, where more bloodied bandages can be found, confirming that Kellogg is encamped within the fort's walls.
The Sole Survivor must enter the fort, either through a roof hatch (which is guarded by a myriad of turrets), or through an unguarded door in the underground parking area.
The Sole Survivor will discover that the entire fort has been taken over by a group of synths, largely confirming that Kellogg is working in some way with the Institute.
After the generation 1 synths are dealt with, the Sole Survivor travels deeper into the fort, down by use of an elevator, and eventually into the command center.
It is within this command center that Kellogg will finally be confronted, in which a short exchange will occur between him and the Sole Survivor.
No matter the dialogue choices, Kellogg will become hostile, and he and his synth bodyguards must be dealt with in order to leave Fort Hagen alive.
After killing Kellogg and his guards, Kellogg's terminal password and his enhancements must be looted from his body, as the password will need to be used in order to access a nearby terminal and unlock the mag-locked doors leading out of the fort, and the brain enhancement specifically is needed to progress into the next segment of the quest line.
Dogmeat has the scent. I need to follow him, wherever he goes, and hope he ends up leading me straight to Kellogg.
Search for clues to Kellogg
Check on Dogmeat
Dogmeat has led me right to an old military base called Fort Hagen. Is Kellogg inside? Only one way to find out...
Find a way into Fort Hagen
The main entrance to Fort Hagen is blocked. I need to find another way inside.
Search Fort Hagen
I've made it inside Fort Hagen. Kellogg has to be in here... somewhere. But is Shaun with him?
Kellogg is here. He's been taunting me over the loudspeakers. Time to confront this asshole, face-to-face.
Search for more information
Kellogg is dead, and Shaun isn't here with him. I need to search around for some information that may lead me to my son.
Discuss Your Findings with Nick
Shaun is in the hands of the Institute. I need to find this place and rescue my son, but on order to do that, I'm going to need some help. I should talk to Nick Valentine and see what he knows.
Discuss Your Findings with Piper
Shaun is in the hands of the Institute. I need to find this place and rescue my son, but on order to do that, I'm going to need some help. Nick suggests we talk to Piper and see what information she might have.
It would seem the only person who knew the way into the Institute was Kellogg... and he's dead. But there way be a way to access his memories. Doctor Amari in Goodneighbor may be able to help.
Kellogg is fast, durable, and will cloak when taking damage to heal during in combat. Consider taking an NPC like Nick Valentine along for the ride, to help find and eliminate Kellogg. However, if the player character is powerful enough, it is possible to kill Kellogg before he can enter stealth.