Losing Companions in Fallout 4 by Siding with the Institute

So you‘ve embarked on an epic journey through the post-apocalyptic Commonwealth in Fallout 4. During your adventures, you‘ve forged close bonds with a diverse cast of companions who fight alongside you. But now you stand at a crossroads that will reshape the fate of the region – ally with the shadowy Institute or oppose their sinister synth agenda? This choice is not made lightly, as it means turning against the Railroad and Brotherhood of Steel to cement the Institute‘s dominance. What is the cost of sacrificing conviction for the allure of the Institute‘s power? Potentially losing friends who stood by you when no one else would.

Why Companions Disapprove of the Institute

Before analyzing each follower‘s reaction specifically, it is important to understand why siding with the Institute often leads to irreparable damage to relationships you worked hard to build within the Commonwealth.

The Institute‘s morality is dubious at best. With the ability to create sentient synthetic humans at will, the shadowy techno-cabal has frequently abused this power in reckless or disturbing ways. Experiments like replacing people with imposter synths to monitor surface communities violate fundamental ethics. And the infamous "Synth Retention Bureau" ruthlessly hunts down any rogue synths seeking freedom or autonomy from their creators.

You embrace the destruction of opposing factions. To complete the Institute questline, you must follow Father‘s directives to eliminate the Railroad and Brotherhood of Steel by any means necessary. This means wiping out entire factions many of your companions are personally affiliated with or sympathetic towards. They cannot abide such outright destruction – especially for the morally questionable goal of consolidating the rule of what they view as amoral tyrants.

You betray principles your allies stand for. Those who fight alongside you against threats like raiders, super mutants and feral ghouls typically possess noble motivations underpinning their cooperation – belief in freedom, opposition to suffering, protecting the weak etc. The Institute often directly opposes such values, forcing companions devoted to these causes to see you as having betrayed both them and those principles.

With these reasons in mind, let us analyze how each companion reacts if you ultimately cast the fate of the Commonwealth into the ruthless grip of the Institute scientists by completing Nuclear Family:

Deacon – Hostility and Exile

As one might expect, few companions oppose the Institute more vehemently than Deacon – one of the most senior agents in the Railroad dedicated to freeing synths from bondage. Throughout your travels, Deacon not only lends you his rifle on many adventures, but also elucidates on the implications of sentient machines and how the Railroad strives to peacefully coexist with all beings seeking freedom.

If you ultimately betray those ideals by pledging loyalty to the very faction that manufactures such beings as slaves, Deacon‘s affinity for you transforms into outright hostility:

"Deacon vilifies the player character for their decision and from that point on, he refuses to travel with them any longer." (- Fallout Wikia)

Losing Deacon‘s companionship forever is one of the definitive consequences that demonstrate the larger repercussions of choosing the Institute‘s vision of the future over that of their enemies. No amount of affinity or friendship can overcome such a fundamental schism in values between you and a lifelong synth sympathizer.

Paladin Danse – Exiled or Executed

As the Brotherhood of Steel‘s most stalwart champion encountered in the game, Paladin Danse epitomizes their creed of securing powerful technology from those deemed unworthy of wielding it responsibly. Should you use your inside access within the Institute to launch a surprise attack against the crew of the Prydwen, Danse will never forgive this ultimate betrayal:

"If Danse is a companion at the time the Prydwen is destroyed, he will exit his power armor and attack the Sole Survivor on sight before fleeing, never to be seen again." (- Fallout Wikia)

In fact, even if you maintain good relations with Danse but complete the Nuclear Option quest for the Institute, the Brotherhood will order his execution – forcing you to either kill him yourself or convince Maxson to exonerate him as an exile. Siding against his brothers-in-arms leaves no room for Danse in the Commonwealth.

Losing the Brotherhood‘s most valiant warrior is often the price one pays for elevating the Institute over all other powers vying for control. Danse remains loyal to his cause to the bitter end – even if that end comes at your own hands.

Mixed Reactions among Other Companions

While Deacon and Danse have clear affiliations that make their condemnation and abandonment of your Institute partnership unambiguous, other wanderers of the Commonwealth fall along a spectrum of approval levels:

Strongly Disapprove

• Hancock: The Ghoul Mayor of Goodneighbor harbors no love for the Institute‘s meddling in the lives of the people. But his personal code of honor still allows him to remain by your side – though he will staunchly oppose their morally bereft vision for humanity.

• Piper: As a reporter and defender of Diamond City‘s citizens, Piper despises the Institute‘s authoritarian control and hidden atrocities. She will voice harsh condemnation of your decision, but can still be convinced to travel together due to her faith in you.

Accepting Pragmatists

• MacCready: The mercenary MacCready remains indifferent to ideological conflicts as long as you provide ample compensation for his crack shot. He will follow you even if that means the Institute now signs his checks.

• Cait: With little interest in anything more than picking her next fight or score, the cage fighter Cait shrugs off the broader impacts of your choice and sticks around for mayhem and caps.

• Strong: As a Super Mutant, Strong has no dog in the fight between human factions. He will continue bounding into battle at your side so long as you provide worthy foes to crush.

Ideological Supporters

• X6-88: The imposing Courser was literally built to serve the Institute. He will support you without hesitation if you pledge loyalty to their collective cause of advancing technology and knowledge through unfettered research.

• Nick Valentine: Despite being a prototype synth himself, Nick places pragmatic order and stability for the Commonwealth over ideology. He will back the Institute if you believe their vision can truly make life better for people in the long run.

Companions – Institute Support Impact

Was It Worth the Loss?

As this analysis shows, although most companions can still stomach traveling with someone partnered with the morally questionable Institute, you definitively and permanently lose Deacon and Paladin Danse. These losses sting deeply – both in terms of their formidable prowess in the field, and on an emotional level after bonding over so many battles.

Ultimately only you can decide if such sacrifices balance out the formidable powers now at your fingertips by allying with Fallout 4‘s most ambitious and ruthless faction. At times, victory demands heart-wrenching compromise.

But I hope this guide helps you fully appreciate the implications before you make that game-changing leap to bind your fate with the Institute!