So I have a question as to whether I am being a bad teammate. I have been in a campaign for a few months now and we have three core players who are almost always there and a few others who come and go. The 3 core players are myself(armorer/eldritch knight), a firbolg life cleric, and a tabaxi warlock of the fathomless. My character is a neutral good knight in shining armor willing to get between others and danger. Our cleric is similar and our warlock is the tricky type who tries to steal things from(mostly) our enemies. Generally we work pretty well together but our cleric is busy for a week or two and we have a guest player who plays a paladin. We agreed to help a dwarf whose home city is under the control of a pirate(naval campaign setting) who is trying to take over the local empire. We have had run ins with his followers and don’t like how he runs things so we agreed to help. So the dwarf says that under the city is a dangerous group of monsters that are sealed away by a sword the pirate has and we’re told if the dwarves don’t do as he says then he will unleash them. We agree to take care of the monsters. This is where the cleric has had to step back for a couple weeks. We get to the city, dwarves are acting weird and give us fancy names warlock is Vessel, I am Destroyer, and paladin is Herald. It’s creepy and pretty obvious that something is mind controlling them, because if they offend us even slightly the. They jump off bridges and stab themselves. We get down and start to fight through monsters behind the barrier and the dwarves introduce us to the Hierophant who leads them. Some kind of undead whale creature who is totally not mind controlling them and ordering about undead Beholders. The Hierophant tells us there is a dragon below that claims to be a god and if we kill the dragon the hierophant who IS a god(according to itself) and it’s master, who is some kind of Kraken, will reward us with the Infinite. Our warlock is onboard wanting to kill the dragon as is the paladin. I am not. I am 96% sure we should kill this creature and that will free the dwarves but they convince me to go down and I agree to go down on the condition to ask the dragon’s side of the story first. We get down and this dragon says he is the brother of Bahamut ant Tiamat and is tasked with keeping extraplanar threats, like the Kraken, from invading the material plane. So at this point I say no, not killing the dragon but the warlock and paladin say they are going to anyways and so I leave the two of them to fight alone. I am pretty sure our cleric wouldn’t want to kill the dragon either but not 100%. Am I being a bad team player by ditching the others here? (Btw the fight hasn’t actually happened yet)

I'm not going to say whether you're being a bad team player, but the whole dragon/kraken/mindcontrolled dwarves thing sounds like a questionable situation to be sure.

Did anyone in the party try to do an Insight check on any of these creatures to see if they were being deceptive? Depending on your levels, the Paladin might have access to Zone of Truth.

I realize I didn’t clarify a small detail. Later on I did an arcana check and realized the Hierophant is an aboleth that with mind control abilities so that seemed pretty clear and the every time I brought up that this all seemed shady the others brushed it off. I admit I didn’t insight check the dragon. As for the paladin, they are a guest player so I don’t know their spells or skills.

It's hard to tell, it seems just a misalignment of objectives tbh.

I might be reading into things here, but a Fathomless Warlock, wanting to work for a guy that has a Kraken as a master, makes a lot of sense. And the names - Vessel and Herald vs. Destroyer. Does your DM does that thing where he plans story bits with some players and leave some outside to create surprises or smth like this?

Don't think you are doing anything wrong, tbh. But it might end your campaign if the guys get killed or, even, just bc what is the sense of you guys being a party when you're in completely different wave lengths.

I had this scenario once, where my fighter was misaligned with the party (they wanted to kill someone for money, bc a wraith asked them to and my PC was LG), so I came up with the bullshit excuse that he didn't agreed with the job, but would carry on to protect his teammates. In the end, it felt like shit.

The DM does talk to us privately if something happens the rest of the party doesn’t know about but I haven’t seen any planned story bits where people already knew what was going to happen. He does like to foreshadow, for example one player summoned a future version of themselves and we learned that in his future the warlock turned into a tentacled monster, the cleric was eaten by a blue dragon(he is currently friends with a blue dragon wyrmling, and I simply disappeared(I may or may not have a permanent bag of holding and an artificer infusion that let me make another). 

I suppose the biggest thing is that I just feel really conflicted about the whole scenario. He wants to protect his friends but there is no way he is killing a dragon that may or may not be a pseudo deity tasked with keeping dangerous extra planar creatures creatures away. I am leaning towards running back and shoving a box down the Aboleth throat and thunder waving it so it and the 50 glass vials of acid break inside its mouth and failing that using the bags of holding, which would be epic if either of those worked but…

I'll begin by saying that you're not a bad teammate. The fact that you've bothered to ask tells me you have nothing but good intentions and a willingness to learn, though there is the obvious caveat of us only knowing your side of the story.

Here's some suggestions to think on:

1. Attempt to go ahead and convince the dragon to tell their side of the story. Assume the worst: the dragon knows you're coming, it is intimately familiar with its lair and surroundings, and that anything it says is for its own self-preservation. Talking will cost you nothing, and if combat breaks out, you defend yourself.
2. You don't have to like the choice, but you are in an adventuring party to achieve a common goal. Protect your allies, and maybe convince them to spare the dragon when it's on its last legs for interrogation. Make them meet you half-way.
3. If the choice is that bad, temporarily or permanently retire this character and bring someone else along who aligns with the party's goals.

I strongly discourage you "shoving a box down the Aboleth throat and thunder waving it so it and the 50 glass vials of acid break inside its mouth and failing that using the bags of holding, which would be epic if either of those worked." It's a massive assumption that this will be allowed, let alone work, and even then you're asking the DM to run two encounters that may be hopeless for either 'side' because they were engineered for all party members being present, unless yours happens off-screen, so to speak. I can see a TPK in two acts happening there, and that would be poor play.

Let us know what your DM's said and how it turns out. I wish you nothing but the best.

I think that the first thing you should  do, is explain again, outside of the game, to the other players that your PC would not do it, and give them time to realize they may not be able to complete the quest without your help.

This is your character and you should play him as that. If the other characters actions do not fit with your character's morale's, that's alright. But also, your character (I think at least) would probably not abandon the other PC's.

You can leave the party, but make sure that the other real people at the table understand why your character is temporarily leaving the party, and make sure they are ok with that.

Quote from ElderCarr >>

So at this point I say no, not killing the dragon but the warlock and paladin say they are going to anyways and so I leave the two of them to fight alone. I am pretty sure our cleric wouldn’t want to kill the dragon either but not 100%. Am I being a bad team player by ditching the others here? (Btw the fight hasn’t actually happened yet)

 Let them fight it alone.

Then step in when each of them falls unconscious and drag their bodies out to safety.