One of the things about the setting is communication. When it comes down to it, there are a few methods by which this is achieved.
The most common way is to speak a common universal language. This language, in 21st century English, can be translated in different ways: Common, Trader's, Universal, and even...English. In spite of it not being instantly recognizable as English to a 21st century speaker (it's loosely akin to an Old English speaker being thrown into the modern day world of English), the language most widely spoken is derived from multiple sources, including a descendant of English.
Languages of course are incredibly diverse. Regions isolated develop their own language with enough time, and each world had multiple languages rather than one universal language. Different dialects, different meanings, and so on and so forth, so in spite of only a handful of races, there are thousands upon thousands of languages in existence.
However, by having that common language, communication is much easier to establish, and this is at a time where people have had enough time to develop that common ground, a language which is REASONABLY easy to learn, especially for a 21st century human who just has to learn the evolution of his own language and how alien words got introduced, more or less, and mixed in.
Having a common language is a great way to ensure that if all else fails or malfunctions, communication does not break down entirely. (As in, if universal translators don't work, you can still speak to one another manually. This is one reason that another common position on ships is a linguist, whose job is to speak fluently as many languages and dialects as possible, in case Traders/Common/Universal/English isn't spoken.)
THAT BEING SAID, this is not always a solution available. The next-best thing is "auditory and visual augmentation enhancements": implants. These are a self-contained computer which link to the auditory and visual sections of the life form in question, and form a pathway. When they hear a language they don't speak yet their internal computer recognizes, the computer will, with a delay, translate it into their ears as something they do.
When they wish to speak a language they don't actually speak, they essentially use what amounts to their eyes to link together an invisible-HUD that is, "this is what I want to say", and the computer then tells them how to say what they want with the correct pronunciation.
This is the setting's first equivalent of a Universal Translator, allowing for Translation Convention. The idea here is, sound (along with visual cues when necessary) is relayed to the device, which then translates it into something the user can understand. (For instance, different regional accents of a foreign language might be translated as different accents of English, anything from a Chicago to different regions of Texan to various English to Australian accents.)
In the HUD of the user's visuals (as in, for humans, we see from our eyes and this would be like a first person shooter with a text HUD which we can then scan with our eyes for the relevant information), the user will think what they want to convey, and the device will tell them through a combination of auditory and visual cues exactly how to say what they are intending to convey, so long as the computer within recognizes both the language of the user and the language of the recipient.
This is something which works great especially when the implant is on both sides (as that reduces the chance of error), but something which usually only has a 100% success rate in a face-to-face conversation. (It also works for written words, by the way, in a way similar to how subs work for anime and the like--the language seen is converted into the text of the user's target language.)
For long-distance communication, an external version of this system is used. The communication is delivered, and then the system in the transmitting device attempts to translate it with a delay built in. This means that, say, ship to ship communication between sides is not instantaneous if there is a language barrier. The speaker speaks the language, the computer processes it, and then tries to emulate the voice as best as it can within the language it's being translated to.
This then can work in reverse, with a message sent, the computer taking time to translate it into the target language, and sending it to the other side. It is less-than-optimal (another reason for a linguist on ships being that having one, they can speak faster than the computer can translate often), but it ensures that there aren't catastrophic communication errors from bad translation.
When this is still not viable, then the most basic, fundamental version of the universal translator is simply, the language of the speaker gets shown in written words, translated without audio, with a significantly higher delay for extra time to process. While it takes much longer and is a far more basic means of translation, it is also the least-prone to failure.
But that being said, just speaking English, as it were, is the simplest solution. (And by English I mean the language equivalent thereto.) If this were a show proper, heavy usage of Translation Convention would be given, in that while what they were speaking wouldn't technically be 21st century English, for the sake of viewers, we would hear it as being 21st century English.
However, at the very beginning, there would be a scene from the viewpoint of the existing crew and the viewpoint of the protagonist. In the crew's viewpoint, they would be speaking English that we'd understand, and the protagonist would be mute, making gestures with his hand but not speaking, with them taking time to figure out his language is 21st century English. In the protagonist's viewpoint, he would be speaking English that we'd understand, and the crew would be mute, making gestures with their hands but not speaking, and this would last until they could synch things up, after which point it'd become irrelevant--
The protagonist would receive the implant, become familiar with the translation technology, and start learning the modern English without usage of the translator, something which while difficult is not impossible and with the aid of the translator would only take a short amount of time for someone of his intelligence and skill to get a basic grasp of. Thus explaining why everyone would be able to communicate with him.
I also extrapolated upon the computer I mentioned. Obviously, I don't mean a singular computer system is all a gigantic ship has--however, they do have only one AI, as in, full artificial intelligence proper life form of its own, per ship. Said AI has access to most of the ship's on-board computers, and thus, is able to access most systems, albeit with checks, similar to as if they were a human user.
Basically, every single part of a ship would have a different computer system controlling it, linked to the others. You know, so that if one thing fails, everything doesn't. These links can be strengthened or severed as needed, and it's akin to networking computers at, say, an office work place. At its higher level, you can take control of one computer from another computer. At its lower level, the computers might have a shared drive where information can be stored but are otherwise separate. Or even altogether absent from each other with the only thing they have in common being that they're in the same building, so to speak.
The AI is essentially a program. It has its own personal computer, but it can access other computers throughout the ship as necessary for its duties. It is also able to some degree operate many systems automatically, albeit in a limited capacity. (Mostly, it can control backups to make sure the crew's lives are saved in case of catastrophic failure.) These systems are fairly universal across any ship.
Also worth mentioning. Yes, the future does have internet. Said internet is actually the de facto method of communication. Think of communications between ships as essentially phone calls with visuals: faster than the internet, but also more limited in what you can share/give/communicate/etc. Think of the speed of travel as being the speed vehicles in our world travel: significantly slower.
Then think of the internet in the context of those two. Much, much faster to send an email than to send snailmail. Communication through text messaging is faster than communication through emails, but communication through emails is easier and allows for more to be sent. And in the future you can kind-of see how that would work.
Information is compressed, transmitted, and stored in ways such that this is not at all surprising. The internet is a vast, cross-galaxy network with servers in countless numbers of planets, moons, stations, and what have you. Every ship can be thought of as having galaxy-wide wifi in that they can connect to a source and from this source they can put the information where it needs to be put.
There's a ton of security in place, and you can have private servers and such, and there's a bunch of measures taken including AIs whose entire job it is to keep out malware. (Artificial Intelligence inside of computers can detect and eliminate viruses much better than any human could.) And, yes. Humans who can check on the AIs to make sure they haven't gone rogue or been hacked or the like.
Now, just like in our world, this does not mean information is inherently secure. Information can be intercepted, information can be hacked, information can be corrupted, and it is. We're talking about a setting with hundreds if not thousands of factions fractured about the galaxy/galaxies in that you have multiple factions on a single planet and factions controlling dozens OF planets and so on and so forth. They are going to try and fuck with one another.
And there are going to be people who mess with the system. Just because they can, or because they're extremists with a vision. But for the MOST part. The internet is one of the best ways for the universe to be linked to one another. You can have conversations across most of known space in a short amount of time with minimal delays.
There are many main hubs for the internet, superstations as it were, and one of them is on the station/ship in fact, allowing it to always be in touch with anywhere, essentially. I am not well-versed in technology to see how feasible a lot of this stuff is. So I'm sure if I ever made it a story proper I would revise all of this and get it more grounded in reality with better technobabble that is more sensible and plausible, but I think that the general idea I have is more or less good and would last.