: Prepare for more after the "ending"? In my story, there's this big bad, who needs to be destroyed. That is the main goal for about the last third of the video game. So the group of heroes

Preparing Your Audience

To inform your audience that defeating the antagonist is not the end of the story, you can use a combination of foreshadowing, unresolved plot hooks, audience expectations, and narrative focus. By providing compelling stories and dramatic tension outside of your protagonists' conflict with the antagonist, you can carry the story far beyond what would normally be the climax.

Foreshadowing

First and foremost, you need to provide some indication while telling the story that anticipated climax is not the end of the story, but simply an important milestone. Otherwise the last portion of your story will fall flat as it will feel like an over extended denouement.

You should provide enough hints to establish that the conflict will not be resolved simply through a confrontation with the antagonist. In your particular case, be sure that both the audience and the characters learn - or at least have reason to suspect - that your villain will eventually be resurrected if further steps aren't taken. This way, when the villain is killed, enough dramatic tension will remain to carry the story forward and hopefully build towards the final climax.

This is important to do even if the last part of the story is intended as a surprise twist. Revealing a secret out of the blue without any hints will feel like cheap; instead, make your hints subtle and ambiguous so as to make the audience feel cleaver when they put it all together.

Unresolved Plot Hooks

Many people enjoy seeing the resolution of various plot points. (I'm sure this is especially true of gamers with a "completionist" streak.) With enough loose threads, people will remain invested in the story just to see those threads tied up. Be sure that a few remain when the anticipated climax occurs.

In your particular case, I'd suggest the protagonists not discover how to leave the villian's dimension until after his death. You can then reveal the villain's potential return while they are searching for a way home, creating a dilemna for them: do they focus on getting home alive or stay to protect the ones they love?

Do avoid leaving too many loose threads, though, as that will risk making the story either incomprehensible or simply unfocused.

Audience Expectations

You can leverage your audience's expectations to signal that the confrontation with the antagonist is not the end of the story. The specifics of how to accomplish this will vary depending on the medium, but in essences you should leave your audience thinking, "This can't be the end yet!"

In the context of a video game, here are some possible techniques:

Have the confrontation occur earlier than normal; if a play-through of most games in your chosen genre take 20 to 30 hours, have the confrontation occur somewhere between 10 to 15 hours.
Leave some content inaccessible or unexplored as many players will take this as a hint that the upcoming boss is not the end of the game; be careful not to overdo it, though, as it can become frustrating or obvious
If you have a progression system, make it so the characters still have a fair amount of development left; for example, in an RPG with a maximum level of 99, encountering the boss at level 40 will be a good sign that there's more to the game left.

Narrative Focus

Lastly, one more technique you can use is to focus your narrative on something other than the antagonist. Make their defeat serve as an opportunity to further the plot instead of being the plot's final resolution. For example, if you focus on the struggle for survival, the villian's defeat can show that the characters have developed some confidence and mastery of the environment. If you focus on the interpersonal conflicts between the characters, the villian's defeat can show that they've learned to work together. In either case, though, there can still be ongoing conflicts that haven't been resolved.

Alternatives

Given what you describe of the story you wish to tell with your game, I would suggest you consider alternatives to a single, linear plot. Other answers include great suggestions, such as:

Reserving some of the ideas as an introduction to a sequel instead of a conclusion to the original game
Using multiple playthroughs to show different perspectives, allowing for a shorter, focused denouement.
Provide the extra stories as bonus content

Personally, I strongly recommend the last option. Not only would this give players who are well invested in your game a chance to play more with their favorite characters, but it would allow you to tell additional stories with somewhat independent arcs.

Some Examples

What You Can Do

I can think of several games that have extended stories that you should consider.

The first is Tales of Symphonia. The story starts off with our young heroes on a journey to "regenerate" the world. At the very end of their journey, they discover a dark, terrible secret that is one of my favorite plot twists ever. There are a few hints that the heroic journey is not the end of the game:

Some of the more cynical characters aren't completely sold on the value of the journey of world regeneration
There are a number of mysteries about the world; in particular, the nature and origin of the desians who antagonize the heroes
The journey reaches its conclusion early in terms of hours of playtime and character's progression

Another to consider is the original Xenoblade Chronicles. Much of the game is spent fighting the "mechons" - mechanized monstrosities. As you become closer to confronting the leader of the mechon army, there are many of the trappings of what would normally be the end of the game. However, once this villian is defeated, a new more powerful antagonist emerges. This is far from a cheap conceit, though, as the villian's presence and plan are eluded to throughout the game and help bring together a lot of the disparate elements that previous felt like random world-building.

What You Shouldn't Do

I can think of two examples of that illustrate what you should avoid.

The first is the movie Castaway starring Tom Hanks. Though good in many ways, I feel the movie has a fatal flaw: a lack of focus. The movie is roughly split in half between the protogonist's life before and after being stranded on a remote island. It felt like two separate stories instead of one. It would have been better if the focus had been placed more on one of these two parts of the story. It could have been about his struggle to survive and maintain his humanity or it could have been about his struggle to put his life back together in the aftermath. By focusing on both equally, the story falls flat.

The second example is the game Tales of Legendia. As with Castaway, there are essentially two stories with the same character(s). In the case of Tales of Legendia, the two stories are largely distinct. The story takes place in the same location with the same characters, but instead of being a continuation of the first act, the second act follows an unrelated story arc with an unrelated conflict. The first act (which I felt was good and all that Tales of Legendia needed to focus on) was about the struggle to secure an island that was, in relativity, a giant ship. The second act was about the emergence of a dark and mysterious entity; though it had some of the best character building moments, the second act lacked the grandeur and excitement of the first so it became a major drag. (It doesn't help that the second act has you re-tread most of the dungeons from the first act.)

Conclusion

In the end, the most important thing to consider with your idea is how the content will fit together into a satisfying story arc. If it is all organized as a single plot, but the dramatic tension doesn't build properly throughout, your story will suffer. Ensure that the extended "ending" is compelling and adds to the overall story or keep it separate so that your audience can have a satisfying, self-contained story to enjoy.

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Leave yourself room for a sequel

By wanting to give everything off the bat, you may block yourself from being able to create a sequel and bringing back those characters. I will echo Amadeus' answer to keep the epilogue short and focused on the main points for the future (future=sequel).

Its ten years later... The character returns to this place because of disturbing rumors. What happened in the meantime? Who is still there? What did they do? Then you have a full game to explore the repercussions of what the character did... Leaving you open for even more action!

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How can I prepare the player for that?

You don't.
It's quite simple: you don't want to prepare your player throughout the game of this aspect. You want it to be something special. Most games end when destroying the Big Bad End Boss, but you want to make your game special by giving your players more after the normal goal. There are some ways to hint at extra content, such as currently inaccessible landmarks if you insist on making it obvious that something will happen after the boss is defeated.
Think about making a second playthrough
But you should think about whether you want to make this the last quarter of the game or whether you want to make it a second playthrough. Look at other games for examples of how this can be done effectively. my favourite example is Nier Automata.
Following are spoilers for Nier Automata - you have been warned.

In the game you first start controlling the main character on her journey to kill the bad guys. In the end she manages do just that - kill the bad guys. It's a happy ending with the bad being dead and the good being not dead. The player feels a sense of accomplishment and thinks he is done.

But then the game tells you that there are huge parts missing and that you should definitely play a second time.

So you play a second time from the point of view of her helper. There is a lot of nostalgia, seeing everything again, but from a different point of view and there are lots of details shown that make you think that the solution may not have been as perfect as you have thought after the first playthrough.

After that the game tells you that there is still something missing. And this is where your idea comes into play.

The third playthrough continues from where the other two left off. And trust me, it's not a happy ending this time. There are lots of aspects uncovered, little things that were hidden in the other playthroughs, a new character is introduced and there are difficult decisions to be done by the player that will change the ending you get.

A second/ third/ ... playthrough allows to focus on different characters
By making your exposition a second playthrough you could switch your point of view and you could explore the problems that arise from the previous solution. If you want to look at multiple characters you could easily make multiple such playthroughs. They are basically just additional chapters, but Nier Automata managed to make the player feel like they already beat the game and then they had the chance to continue and find out what happened afterwards and how the story continues for the main characters.
Hints at other playthroughs could be shown by using different unaccessible story bits - treasure chests that can't be opened, paths that can't be visited, people that can't talk (yet), ...
The game did have some spoilers. There were certain treasure chests that the main character in the first playthrough couldn't open, though it was never completely clear whether you would simply get a new ability at some point or whether you had to use a different character. The second playthrough established a few loose ends that needed to be tied together by showing different aspects and motivations of evil enemies. You suddenly wanted to know more about them and get to know them - and if you were careful and looked around you often found out that you didn't really want to hurt them. But you had to. For the greater good... Right...?
Make your game feel special by giving your players something more to do after playing through the game
You want your players to feel the same way. You don't want to make it too obvious that there is more at the end and you want your game to feel complete after defeating the final boss. But then you want to give the player the chance to explore more if they want to get to know more.
Making it a different part allows your players to decide for themselves whether they liked the original ending or the bonus content more
This gives your player the chance to change from a simple Be the main good guy!-story to a fascinating What are the ramifications of my actions?-story and may leave your players with a better feeling. Those who liked the first ending can simply say "I didn't like the additional stuff", while the other players can say "I loved how the story picked up the pieces at the end and went in a different direction". You will make both sides happy.
If you instead made this a chapter you would force everyone to accept the second ending. Leaving it up to your player will make it easier for them to feel good remembering your game. There are different types of story-tellers and there are different types of story-listeners.
Possible ways to hint at extra content
If you want to hint at a second playthrough or an additional chapter you can use the approach mentioned above. Simply place items, locations or characters somewhere that are inaccessible to your players and let them figure out that they can get there and see more about your world once they are done. Maybe the Big Bad Evil Boss had a special item. Or your characters gained new abilities. Or maybe the destruction of the Boss changed the landscape for whatever reason. Or maybe people are just suddenly more willing to talk. Or people could suddenly move around more freely and someone from RandomCity1 could help you with a little sidequest in ChanceTown3.
There are many possibilities and even if you simply add a new town "12 years later" you can get your players to enjoy the additional bits of aftermath that you want to show them.

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I don't know about video game fiction; in novels and movies, epilogues are typically very short, and used for the explanation of the future. In a movie, just a few minutes (2 or 3 pages, about 2% of length), in a book, perhaps 4% or 5% of length.

To accomplish what you want in a standard storytelling mode, you need to make killing the main villain not enough to end the danger: The villain has set into motion magic or technology that must also be stopped.

That is the thing your characters can discover before they have their confrontation with the villain and destroy him, he has a "dead man switch" so if he dies, others events are triggered to destroy the world (or something like that, cause great suffering).

So perhaps, knowing this, they don't even want to destroy him, they want to capture him, but on the brink of failure in trying to capture him, they kill him. That victory is now only a partial victory and they know it. Do something in the game so they do, the spirit of the villain splits into five parts and zoom away for parts unknown, evils no longer imprisoned by his life force. Easier to defeat, but if allowed to grow, they may join forces again and be worse than the main villain.

So now off they go to complete the mission and exterminate the pieces, wherever they hid. (They may know where, or may need to discover where, your choice). In the process they discover an escalation of other truths (the secrets you want them to know), from small to large, with your biggest secret the last, when they have cleaned up the final fragment of evil spirit. Perhaps that last threatens the life of the one side character that saved them all, for example.

Then victory is complete, the hidden hero gets his due recognition and gratitude, the clouds part for the first time in years and golden sunlight brings vibrant color to the forests and gardens, and life to the lakes and streams, and joy to the populace.

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