I always thought it kinda off that when you have the canons all ready to go and the institute already knows of your role in the Minutemen, that there was no option to take advantage of that instead and let the player use the Minutemen method of dealing with the Brotherhood that way instead of wasting tons of institute resources.
So I'll propose how such an idea goes down.
Dialogue: When you talk to Dr. Li/Evan (for this dialogue, I'm assuming the Former), instead of "what do we have for a plan b", if you have completed old guns a different option will appear.
"I've got a plan b"
"We don't need a 'plan b'"
- You're right. "Okay you're right. It was a stupid idea anyway. Continue." (aborts this path)
- Like it. "Don't worry, you'll like this." ("Persistent, aren't you? *sigh* Okay. Out with it. then. What is your proposal")
- Director "Which one of us is the director here?" ("Being the director doesn't automatically make you an indisputable king, you'd best learn that quickly. Although you are right in some regard: I am obligated however to listen to what you have to say. So out with it. What is your proposal?"
- Resources "Are you sure? My proposal will waste a lot less resources." ("I will admit, this current plan is going to put a heavy drain on our gen 1 and 2 population and armament. Something we'll no doubt need for other things. Okay, you have my attention. What is your proposal?")
- Know Minutemen "What do you know about the Minutemen?" ("The... Minutemen? Well, if my ancient history is up to par, they were a bunch of citizen soldiers. A milita. Or... wait, no. You're talking about the group emulating them. Yes I know of them. I happened to know they happen to have artillery batteries. ")
- Artillery "Why not shoot them down with artillery?" ("Because we don't have something like that. Wait, you're referring to your Minutemen yes? I've heard about that. Question is, why would they want to help the institute?)
- Swat them down "We swat them down with explosives." ("You do realize we'd need a very heavy amount of firepower for that? Even if we'd gathered up all the missile launchers in the commonwealth I'd doubt we'd be able to pull that off. To even breech its armor you'd need Artillery. Artillery.... Ah, I see where you're going with this. You're talking about the Minutemen's artillery, aren't you? Question is, why would they help us?
- Nevermind "Eh, nevermind. It was a stupid idea anyway." ("Eh, alright then. Anyway...) (Aborts this path)
- War with Brotherhood "They're at war with the Brotherhood too." ("Ahhh, good old Brotherhood. Always getting under the skin of everyone they come across. Although I don't doubt you had a role in that too.")
- Doesn't matter "Does it really matter?" (Just so long as they don't get the idea to turn on the institute after this, then I suppose it really doesn't.)
- Brotherhood Gone "They want the Brotherhood gone as much as we do" ("speaking from personal experience, I can't say I blame them in the slightest.")
- Enemy of my Enemy "We're the enemies of their enemies." ("Yes, that does have a habit of forming alliances, doesn't it? Trouble is, it doesn't usually last. Still, since you seem to be in charge of them, I suppose there is some hope that this won't turn on us. At least, not in the immediate future.)
(all: "So let's go over the plan. You get your Minutemen to shoot the Prydwen down with the artillery, the Prydwen falls from the sky, crushing Liberty Prime and any further ambitions the Brotherhood might have had for the Commonwealth along with it in one fell go. This keeps you out of danger, something I'm sure Father will be more than happy about, and this means we do not need to send any synths to Boston Airport. There is quite a bit of merit to this plan of yours, I will admit. Though there are a few issues. First, the entire point of our plan was to send the message that we can turn their own technology against them. That we can appear from anywhere we please, and that if they were to every triffle with us again, there would be dire consequences. The point of doing the job this way was to send a very specific message to the rest of the Brotherhood. However, that message is lost on this proposal. So tell me, what kind of message do you hope to send with this?.)
- Ancient Tech "They will be defeated with 17th era technology and people less equipped than they are. The lesson is that hoarding tech won't help them." ("Hmm... an... interesting message to say the least. Basically the inverse of what we were going for, but no less devastating. Okay, moving on.)
- Unfriendly Commonwealth "The Minutemen will show them that the Commonwealth is not their friend." ("Hmm, yes. If the Brotherhood wants to mount another offensive against us, they'll have to engage everyone in the Commonwealth on top of that. I can see the merit of this message. Moving on.")
- In it Together. "They will learn that when they take on one of us, they take on all of us." ("Not exactly true, and I'm sure Father will disagree with you. But... I suppose under your tenure as Director that will ring more true than it does now. At any rate, it'll have to do. Moving on."
- Nevermind. "Eh, nevermind. Let's go back to the other plan." ("So quick to abandon yours? And here I was actually starting to like it. Ah well.") (Aborts this path.)
(All (sans the fourth): "Next issue is what happens after the Prydwen is down. Knowing the Brotherhood, I highly doubt they'll take this lying down. Once that airship of theirs ship goes down, most likely with whatever elder is accompanying them on board, what's left of the Brotherhood will most likely start lashing out in a vain attempt to get revenge for their immediate loss. How do you plan on dealing with this?"
- Minutemen Capable "The minutemen can handle it on their own. No need for our intervention." ("Well, if you say so. I guess if this works we won't need to actually do anything. Father will be quite happy with this, to be sure.")
- Synth Backup "Send some synths to back us up when the airship goes down." ("And you think the Minutemen will simply accept it, just like that? Well, I suppose if we time it just right, they really won't have much of a choice, and then we can appear the heroes too. Alright, we'll relay them into the castle once the fighting starts. With any luck the Minutemen will be too busy concentrating on the Brotherhood to even notice they're being helped until the battle is over. After that... well, I'll let you take it from there."
- (don't know.)
- Nevermind. "Eh, nevermind. Let's go back to the other plan." ("So quick to abandon yours? And here I was actually starting to like it. Ah well.") (Aborts this path.)
Doing this path will fail "Airship Down" and will start "With Our Powers Combined." WOPC will proceed as normal. If you opted to have the Synths defend the castle, they will show up when the vertibirds start getting in range. Once Defend the Castle is completed, you'll get "Nuclear Family". It will proceed as normal with the exception of Shaun's opening line.
"Ah. There you are. I already heard the news. But of course you would't be here if it weren't a success. The Brotherhood is gone, and by your own hand. Not exactly what we planned, but... it is better this way. I'm glad it worked, but I'm glad you're safe."
There are actually two endings on this: "pure" Minutemen ending, and "Minstitute" ending. Letting the Minutemen handle the counter attack on their own will result in the "pure" minutemen ending. However, letting the institute send synths and coursers to assist in deflecting the counter-attack results in the "Minstitute" ending.
The results:
Minutemen Ending:
- Identical to the Minutemen ending sans any mention of the institute blowing up. Any mention of the Institute blowing up is replaced with news about the prydwen blowing up.
- Minutemen will be what shows up in diamond city, does checkpoints, etc. Companions will act as if the Minutemen won (but will neglect to mention the institute.)
- McDonough will still be exposed and thrown out as a sacrificial lamb, starting "In Sheep's Clothing" The institute will simply not need him anymore (as evidenced by the terminal in SRB he's already obsolete) and decides to throw the Minutemen this bone.
Minstitute Ending:
- Basically combined effects of the Institute and Minutemen endings. News will spread about how the institute helped the Minutemen defeat the brotherhood, and both synths and minutemen will patrol and appear at checkpoints.
- Diamond City will wave Three Flags. The institute flag on the Left, the Minutemen flag on the right, and a special banner right in the middle depicting the Institute logo holding a lightning bolt in the left hand and a rifle in the other, crossing them in a way over his head that forms the minutemen logo. The Minutemen logo will have a blue "star" surrounding it, while the rest of it is white.
- Radio freedom and diamond city radio will tell about how they were helped by the institute.
- Piper will publish a paper lambasting the Minutemen for "selling out to the boogeyman" but will recant it in "Fear the future?"
- Instead of in Sheeps Clothing, you hear about how McDonough suddenly went dead one day, then they found out he was a synth on the operating table.