So Bob would end the war by killing millions of his former brothers in arms? And then expect people to embrace peace?

Exactly my predicament, given his background, would he try to end the war through violence at all? His ship certainly would give him the ability, but he would probably look for another way.

Bob gets poisoned by a honeypot operation on Day 2. The ship vanishes into a government research lab, never to be seen again.

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I changed the question to say, "is it possible for him to end the war" instead of, "would he decide to"

That reminds me of the Perry Rhodan series.

Bob would probably get hungry if he didn't have an unlimited supply of food in his super ship.

Ahh... Food.... Right.....

Considering this scenario is so broken in a dozen different ways, let's assume that one of the ship's weapons can turn enemy fighters into buffets. The ANGRYCHEF3000

The most powerful weapon is the one that never has to be used. Bob should camouflage his new fighter to look like the old one. He will need to be the wisest man in the galaxy to come up with a strategy utilizing the knowledge of the aliens to come to a peaceful resolution. Perhaps the idea of a common enemy could be used to sate mankind's bloodthirst? Would be fun to have the story end with mankind never knowing the power of Bob's ship.

If you have a ship that is literally invincible, then what stops you from flying it into whatever futuristic government centre, and killing all the military leaders?

@SerbanTanasa never to be seen again? If one government got a hold of a super-weapon which is practically undefeatable, either they would try to replicate to use it in the war, or they would use the ship itself to win the war. remember, these are two warring civilizations, and if one of them managed to get a hold of the ship, and without being morally constrained, I'm guessing mass scale genocide would ensue.

This sounds like "how the prime directive" non-interference idea came about. Or maybe the aliens are thinking something similar to "these dogs keep fighting in my alley... I wonder what would happen if I gave one of them a shotgun." Maybe they're wagering quatloos on who gets exterminated first (or funnier like this)

If 1/1000 star systems were inhabited, and you could destroy all the defenses of (assuming this counts as conquering) one system and travel to the next all in one second, it would take about 19 years to do it in our galaxy of 600,000,000,000 stars. Depending on your universe, the logistics are screaming against this being practical, let alone the politics of the situation.

It would also be interesting if he has not just incredible powerful, but incredible precise energy weapons - which would allow him to destroy weapon-systems without harming pilots - he would then just fly by every weapon system and disarm everyone. Even if they build new weapons, just disarm them again. He will get millions of followers, being the peace guy who just destroys weapons and never kills ;-)

This is basically the fantasy world I lived in as a child. I'm even called Bob. :D The problem I think you'll have from a narrative point of view is that invincibility creates no tension.

How long can he live for?

@Falco I thought about using some type of energy weapon that would only hurt enemy weaponry, like an EMP blast, but the aliens would not have thought of this - they would consider it much more efficient to simply annihilate the enemy weapon systems.

Maybe the ship computer is really intelligent and has great scanners, so he can instantly analyze any enemy ship and calculate the perfect power and target to incapacitate without killing anyone ?

Right now Bob's way too friggin' powerful to be an interesting hero. There needs to be something bigger and badder to give him a challenge. Maybe a prototype of the same fighter in the wrong hands?

It's a fundamental consequence of relativity that no one can ever conquer the galaxy. This is actually pretty damn cool.

This also depends on whether or not anybody else in Bob's galaxy encounters these aliens and acquires their technology (through honorable means or otherwise), which could make for some interesting depth of your conflict. If you don't go that route you might want to at least somehow guarantee that nobody else can acquire that technology.

Or perhaps, unbeknownst to Bob, the aliens are using him for their own conquest of his galaxy, conspiracy style. One of their scientists, unknown to their king, may already be in league with one of the sides for some unknown nefarious future plans. Perhaps this is also part of a conspiracy to frame and depose said king, by (new or equally ancient) internal factions that do not agree with his peaceful policies. Etc, etc.

Maybe the ship has an AI that is going along with Bob until the time is right, or a remote control backdoor. Ok, I'll stop now. I'm starting to scratch my chin and stare off into space at my desk.

This seems similar to the Andromeda series. A single ship that is far beyond anything else in the universe trying to establish a world order.

@JasonC why would they need to lie, they can equip a single man with the power to conquer a galaxy, There is no reason that they will be unable to produce a hundred of these and fly them themselves.

@PStag Ooo, well, maybe they are testing a new technology. Or maybe some of the scientists that designed it are part of a secret anti-peace faction that doesn't have the capabilities to manufacture a full fleet just yet. Maybe they have some reason to stay behind the scenes, like a secret alliance with one of the sides and some sort of trade, or they're backing one of the sides and they think they can obtain better control by having the battle be orchestrated by one of the known sides instead of showing their faces. Or something. There's got to be an interesting way to do it! 8-)

(Like in BSG how the Cylons had to stay away to build up their capabilities, then had to secretly infiltrate for a while before launching a full scale attack. Or the Borg sending out small forces and scouts before determining that they really wanted to go for it.) Maybe even these aliens just have a natural drive to stay in the shadows that us humans can't quite relate to (and that could be their weakness and ultimate downfall somehow).

@JasonC Or the king needs to convince his people that they need to invade. It would need to appear as though they were helping, but instead sent Bob on an impossible mission. Next it is their responsibility to overthrow the tyrant Bob. Just like the Syria conspiracies.