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Everyone knows the Brotherhood runs around collecting tech throughout the wasteland, so they should have some pretty cool stuff. But now there's the Institute; an unknown quantity.

Will I miss out on some new weapons, armor or 'perks' by siding with either?

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    Better in what sense? – deutschZuid Jan 5 '16 at 20:38
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    I think "better" could be defined as either worth more caps, and/or overall weapon strength/armor damage resistance. If you clarify which you're looking for, we can better help you. – Broots Waymb Jan 5 '16 at 21:10
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    You can multi-faction pretty far into the game. If you do that, there's only going to be a few pieces of loot near the end-game that you'll eventually have to lock yourself out of. There's several other questions around that cover how far you can go before certain options become unavailable, though not many of them (if any at all) are very loot-focused. – Iszi Jan 5 '16 at 21:13
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    Brotherhood gives you awesome power armor pieces for doing their missions. T-60 with legendary effects. Institute didn't really give me anything, but the vendor is nice. – DCShannon Jan 6 '16 at 23:45
  • As overall damage – Xprokiller12 Jan 7 '16 at 17:29
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I've beaten the game with each of the Brotherhood of Steel and Institute multiple times. I can't claim to have done every single possible side quest for both of these two factions, but I've done most of them. I've supplemented my experience with information from Nukapedia, linked throughout the answer.

Summary: The Brotherhood of Steel gives you a lot of good stuff, mostly power armor pieces. The Institute gives you basically nothing.

Notably, nearly every one of these quests can be done before choosing a side. In fact, the only quest reward here you can't get if you side with the Institute in the end is a T60 Jumpjet, which you can build yourself. You won't lose any quest rewards by siding with the BoS, although you lose out on being able to buy Synth Relay Grenades after the game is over, and the opportunity to kill Maxson and take his stuff.

Required Quests

Let's first look at loot you get from quests that are required to finish the game with either of these factions.

The Institute gives you: nothing.

You literally don't get any items at all, unless you count a paint mod for X-01 armor that you don't get until the quest line is complete.

The brotherhood gives you:

  • Call to Arms gives you Righteous Authority. This is one of the best guns in the game, if not the best. You can easily get this gun within the first few levels and use it for the rest of the game. This quest occurs early, and you can do it regardless of which faction you end up supporting.

  • Shadow of Steel gives you a full suit of T-60b power armor. This suit of power armor is certainly not the best possible, but it's good enough. Depending on how quickly you finish the game, this could potentially be end game equipment as well. This quest also gives you Paladin Danse as a companion. Although not technically an item, Danse is an amazing asset who can single-handedly win a lot of fights.

  • Show No Mercy gives you Vertibird Signal Grenades. These can be used to call up a vertibird, complete with minigun. The vertibird will fly you to any previously discovered location. You can change course or order it to land anywhere along the way.

  • Liberty Reprimed gives you a T-60 Medic Pump, which as a T-60 power armor chest modification. It's not amazing, but if you haven't invested in Science! then you probably have a free slot to stick it in, especially with the free set of T-60 power armor you got earlier.

  • Blind Betrayal gives you a full set of T-60d power armor. This is better than the T-60b armor you already received, and has a nice paint job.

The next quests are Tactical Thinking, which causes you to become enemies with the Railroad, and Spoils of War, which causes you to become enemies with the Institute. So you can still get all the above loot, and then finish the game with the Institute.

  • A New Dawn is the BoS's epilogue quest, after you defeat the Institute. You get a T-60 Jetpack, which ain't too shabby.

Optional Quests

There are a number of optional quests available for each faction. Here again, the BoS gives you stuff, and the Institute really doesn't.

The Insitute gives you:

  • Building a Better Crop gives you 20 stimpacks. Whoopty-doo.
  • Plugging a Leak gives you Liam's Glasses, which is the best thing the Institute will ever give you. They give +2 to Int. Unfortunately, you can't get finish this quest if you've done Tradecraft for the Railroad, which gives you the much better Deliverer pistol. Tradecraft is also needed before you can do the Railroad quests that allow you to build ballistic weave.

There are also some radiant quests that give you common items like grenades or fusion cells.

None of these side quests require that you progress far enough to become enemies with the BoS.

The Brotherhood gives you:

The BoS radiant quests just give you caps and XP.

None of these side quests require that you progress far enough to become enemies with the Institute.

Non-Reward Items

There are certain items that aren't given to the player as rewards, but are still only available during certain, faction-specific quests.

If you side with the Brotherhood, then you won't ever get the chance to kill Elder Maxson while he is wearing his suit of T-60f power armor with a unique Brotherhood of Steel Elder paint job, or while he is wielding his ultra-powerful unique weapon: Final Judgement. Both of these can be acquired by taking certain steps during Airship Down.

If you side with the Institute, then you can buy Synth Relay Grenades from the Institute vendor after the main quest. Also, once you become enemies with the Institute, any synths you summon will be hostile to you.

  • The institute looks like a bunch of bums. What's with them not sharing their loot? – Nelson Mar 15 '16 at 23:49
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    @Nelson The Institute is full of self-righteous, arrogant, selfish jerks. The BoS, on the other hand, is full of self-righteous, arrogant, selfless jerks. – DCShannon Mar 15 '16 at 23:51
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    @DCShannon selfless, riiiight. All they give just a junk to them. – Rusted_Silver Mar 16 '16 at 8:27
  • @NamikazeSheena Not sure I understand that comment. The members of the BoS are almost universally willing to give their lives for their cause, which is what I mean by selfless. That attitude would extend to giving you stuff. Their cause is arrogant and self-righteous, though. – DCShannon Mar 16 '16 at 17:28
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Not true you get grenades that spawn mark one synths, which are not that good but are fun to play with. At the very end when you being down the brotherhood of steel you get T V11 60F bos elder power armor set from killing elder maxon snitch is pretty hard with anything but the fat man, be care full and not lose his body, you also get the final judgement it's super good💦💦

  • None of these are quest rewards given by the Institute, so I didn't include them in my answer. You can get the grenades whether you side with the Institute or not. They're around to be picked up, and you might be able to buy them from the vendor. Final Judgement is also available if you side with the Railroad. You do have a point about these items that aren't rewards but only show up in faction specific quests, though. – DCShannon Jul 21 '16 at 3:52
  • Also, those grenades are fantastic. I usually use them to destroy the Railroad headquarters. They keep Glory pretty well occupied. – DCShannon Jul 21 '16 at 4:01
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You also forget about getting the cool Courser companion, and yeah the relay grenades are actually given to you during a quest. Plus, if you don't side with the Institute, the grenades are pointless. Also, end game you have a lot of synths roaming Commonwealth that can aid you in battle. You also get the best armor, Heavy Synth Armor plus a piece with the chameleon effect on it can be bought. No more legendary farming for it! And of course, the Waser Wifle.

  • X6-88 is not an item. Synth Relay Grenades are not given as a quest reward at any point, as far as I can tell. I just learned that you can buy them from the vendor after the main quest if you side with the Institute, so I'll add that. They continue to be useful up until the point you become enemies of the Institute. Synths roaming the commonwealth aren't items. You can buy that armor either way, it's not dependent on siding with them. – DCShannon Jul 23 '16 at 0:03
  • You can get the Wazer Wifle either way, because you can get Shaun either way. See the Nukapedia article on Shaun. – DCShannon Jul 23 '16 at 0:03
  • Also, if you want a Neverending Laser Rifle - for some reason - you can get one way before the main quest is over: fallout.wikia.com/wiki/Prototype_UP77_%22Limitless_Potential%22 – DCShannon Jul 23 '16 at 0:10
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I'm an Institute joiner, and while the above post is correct in that the Institute does not give much, there are some other positives.

1) INSTANT FAST TRAVEL to the Institute from any outdoor location. It doesn't take you anywhere else like the BOS vertibird, but there's also no waiting and it is in the middle of the map. It's pretty nice when you are overencumbered and want to drop stuff off. You can only fast travel out to the CIT Ruins right below the Institute though.

2) There is a doc in the med/bed bay in the Institute that cures you for free. Sometimes he is bugged at first but there's an easy one-time fix for console/PC both.

3) The Institute has a vendor with ~700 caps available for trading and 1 or 2 legendary synth armor or weapons for sale. There's also a food/water vendor and fresh water fountains in the Institute.

4) Tons of space in your room (at least 14 containers) to store your items.

5) A big DOWNSIDE is you cannot build anything in the Institute and there are NO CRAFTING STATIONS. I put my crafting stations in Hangman's Alley across the bridge.

6) Minor downside: all those viable blood samples and technical documents are useless if you join the Institute (I believe you can save them for BOS missions otherwise).

7) No offense to the BOS, but there are a lot of T-60 armors to find even without the BOS rewards out there. As a crafter, you can make all the same mods too.

8) You can buy unlimited synth grenades (~66-100 caps, I can't remember). Each one pops out a synth to fight your enemy. When the synth dies, you can loot them too.

I play on Survival so it is kind of a pain having to slow travel everywhere after leaving the Institute but I'm used to it now.

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I'm a Brotherhood of Steel fan and I've never been with the Institute, so I have no idea what the Institute has as rewards, but I know the rewards from the BoS from Call to Arms to Molecular Level:

  • Vertibird grenades,
  • Righteous Authority,
  • exemplars T60b torso,
  • steadfast BoS chest plate,
  • (if you have master level in lockpicking or hacking) XO-1 helmet and gauss rifle.

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