I'm going to be talking about a pipedream of mine I've had since I was a little boy. (I think I came up with this around the age of 6. It's been growing ever since.) This game is called Kigen: Genesis, and it's a god game. It allows the player to create an entire world for themselves and others (it allows for multiplayer servers) to do with as they fit. The game itself is mostly a sandbox, but there will be a lot of procedurally generated questlines and the player can make their own goals as they go. Anything from "find out what killed this tribal and put it down" to "topple this empire and build your own" or "make a wagon so you don't have to carry this firewood" to "make a spaceship and get off this rock". The game exists on a 100th scale world, and uses a timescale of 10. Different planets will have different times and be different sizes.

Before you start playing, you must build a world. (Well, there are built-in ones, so I suppose you can skip this if you want.)

FIrst, select game options such as magic/class systems, death preferences and difficulty. By default, there is no real magic in the game, although there are abilities that appear magical from a primitive mindset. (Energy projection, for instance.) There will be a few built-in magic/class systems to choose from if you want a fantasy world. Death preferences determine how death is handled in-game. By default, a dead character is reincarnated a difficulty-dependent time later as an infant and loses a difficulty-dependent amount of level progression, a healthy compromise between respawning and permanent death. You may also choose to straight-up respawn, where you still take time and lose level progress but remain otherwise the same, unless they die of old age and then they either get reincarnated or are dead permanently, which you decide now. Finally, you can choose to make death permanent, forcing you to dismiss a dead character from the party and make a new one to replace them. Difficulty impacts respawn time and experience loss unless permadeath, impacts disease contraction rates, alters progression rate, decides need progression, sways creature spawns and manipulates procedurally generated loot and rewards.

Second, pick a star type and a world distance. Star type is purely aesthetic, determining the star's colour and impacting the colour of your sky. (And how many there are, although binary or trinary star systems are realistically close together.) World distance determines the temperature of your planet, with closer being hotter and father being colder. This can and will impact which regions on your world are livable.

Third, pick an atmosphere type. This determines what species can breathe there, and has a "none" option.

Fourth, select a planet size. This determines planet area and gravity.

Fifth, select the creatures that will be present. By default, all compatible with the world are selected and will spawn in appropriate environments. You can deselect any you don't want, and create your own. Note that there is a "add new creatures" flag, enable that and any new creature you create or download that is compatible and not unselected will be added to the world next time you go there.

Sixth, customize the landscape and place objects, hit "random" to get a realistic template, or hit "procedural" to skip this step. You can get VERY detailed if you want, right down to placing buildings, creatures and plants. Or not, those things generate procedurally in areas deprived of player input. You can also create objects if you want.

Seventh, select a tech base for the world. This determines what procedurally-generated items will appear in the world when the game starts and what tech your party starts off understanding. You select specific technologies, but many have requirements. For instance, you can't select axels if you haven't selected wheels and you can't select metallurgy without fire. This is subject to change in-game, and doesn't change any objects you have already placed. Note that the party's tech selection is entirely separate. Also, this game features reverse-engineering, and any items placed and left in the hands of the AI will speed tech progression in the relavant and pre-requisite technologies. This also works for the player. This is all up to you. You can start with nothing, or everything. You can start with a super-advanced party in a world without any tech. You can without any tech in a super-advanced world. You can start with no tech, but spawn your party next to a pile of super-advanced items. It's entirely your choice here.

Eighth, repeat steps 3-7 as many times as you wish. Once you've created a single habitable terrestrial world, your other worlds can be much further or closer to the star if desired, or else can be gaseous, or wildly different sizes. You may also create moons for your planet (recommended, as they DO impact tides) and even make them habitable. Go nuts, make a whole solar system.

Ninth, create your party. You may make as many characters as 30+2*party level, up to 50 at party level 10, but party level starts at 0 and 30 is where you'll be. Each of these is a full-fledged RPG character, using the ruleset I once detailed here in three parts.* You can also pick generics, select from built-in characters or use ones you made elsewhere, it's up to you. You don't have to restrict yourself to one species, although for practical reasons you should have at least one of each sex for each species included, so finding mates won't be an issue later.

Tenth, pick a spawn point. Just click a spot on the map and hit okay to enter the game.

*1, 2, 3.

This is just an intro, a start-off for a game.
I think the core gameplay is moving around with your party and fighting mobs/missions ?

Will your party have some kinds of craftsmen(women) as well ?

"topple this empire and build your own"

How do you imagine this ?
Are there going to be predetermined missions(maybe randomly picked)/battles until the campaign tells the player that the empire fell, or is the player actively attacking the guards of the empire and if so, is the empire responding ?

This is just an intro, a start-off for a game.
I think the core gameplay is moving around with your party and fighting mobs/missions ?
Will your party have some kinds of craftsmen(women) as well ?

Not quite. You have needs to manage as well. You may also end up with offspring to raise, (which are playable) and jobs to do. (And a LOT of characters, which run on AI when you aren't directly controlling them and can do the boring shit for you.) Crafting is an inherent part of the game. So is inventing. So is teaching and learning. The game has an element of "Civilization" here, allowing you to go from "sticks and rocks" to "bronze and iron" to "steel and gunpowder" or even "energy and nanotubes". The goal of the game (note that there is never a victory condition) can be technological progress, world domination or just survival, it's your decision.

How do you imagine this ?
Are there going to be predetermined missions(maybe randomly picked)/battles until the campaign tells the player that the empire fell, or is the player actively attacking the guards of the empire and if so, is the empire responding ?

Cut off the head and the snake will die. The game features a hierarchy system. Killing a ruler or destroying a commitee or what have you cuts those beneath them off. Some will take their freedom and run, some will find a new organization, some will seek a new master in the same organization. You can split pieces off an organization like this. Eventually, a faction can be destroyed using these means, leaving scattered pieces.

To answer your other question, yes they respond. (And how!) The player does have an infinite supply of characters, though, so if they are determined enough they will eventually break it.

As for building your own, this uses the same heirachy system. You take minions, either give them minions or have them get their own minions. They'll repeat your orders (usually with some slight mutation) for their minions. Cue the snowballing, and hope you don't end up pissing off a bigger faction unless you can do something about it. Easier toppling a pre-existing empire, as you can recruit leaders to gain all their minions at once, with existing heirarchy.

Pt. 2: Creature creation

Unless you are content with the built-in content, you will spend time creating creatures for your usage. This uses a system similar to Spore, only considerably more complex. There are six basic sections. Basic traits, skeleton construction, organ systems, muscle, hide if applicable and stat adjustments. There are specialities available throughout, which cost speciality points. ALL of these have huge effects on the creatures you are creating, and any characters made from them. You will usually be creating one male and one female version unless you choose for the species to be hermaphroditic. These will be mostly the same, but their reproductive tracts have different requirements so it is difficult to make their structure exactly the same. (It'll be impossible for viviparous creatures.) You can create further sexual dimorphism by editing the sexes individually, which although not required is recommended. While the age variations will be generated automatically, you may edit each stage individually as well.

Basic traits:
There are a few basic traits that must be selected before you can move on. The first is chemical base, carbon or silicon. This changes the options available from there on out, and determines your needs. Second is reproductive method, which are separated into two categories, oviparous and viviparous. Each has a number of sub-types, but those are the basic selections. Asexual reproduction is not an option, because it simply doesn't work for higher life forms. (It also is impossible for higher life to develop asexually, due to a low rate of variation and high rate of extinction.) The closest possible is hermaphroditic reproduction, which is an option. Third, select a development method, which has three options: staged growth, hemimetabolism and metamorphosis. (It's worth noting humans use option A.) This impacts the development stages you will be setting later, and the nomenclature used for these stages. (For instance, the young of hemimetabolic species are called "nymphs", not "children".)

Skeleton construction:
Select a skeleton type (endo/exo/hybrid) and begin. Bones are available on the left, different tabs hold different bone types (solid, hollow, reinforced) each of which have their advantages. They have spots where they can connect to each other, just put those together and the game will give them a joint. You can modify this joint if you so choose. (Connection type, size, etcetera.) Build as much as you want. (Or don't, invertebrate creatures are an option, if a bad one most of the time.) This will form the base of your body later.

Organ systems:
After creating a skeleton, you must place organs. Each organ is part of a system, and must be connected to function as intended. Further, the circulatory system will automatically connect to each other system. There's an extended checklist of organs for carbon-based life forms, but silicon-based life forms are much simpler because they do not respire. (They do have circulatory fluid, but it carries nutrients and catalysts.) Among these systems is always the circulatory system, which requires a heart and must connect to every part of the body. Keep track of this stuff, it'll help to know how this fleshy machine works when you have to make it stop working. (It might also help to go take a look at the built-in creatures. Get to know where their organs are, so you know where to drive your steel.)

Muscle:
This part is really simple. Select a muscle type for each body part, adjust thickness. This impacts your stats. Moving on.

Hide:
Another simple part. If your character does not have an exoskeleton, select a form of hide. This is a natural armour, and will always provide you some small amount of protection. In this step, you may also select a coat (if applicable) and you will be customizing the appearance of your species' hide and coat. Colour, texture, patterns, so forth. You can select a base or pre-set pattern, and draw additional patterns on yourself if you so choose. Here's where I suspect most casual players will jump editing pre-made species, customizing their appearance without any risk of seriously screwing up their performance.

Stat adjustments:
Your character's stats have been pre-generated for you based on how they are made. You can apply considerable tweaks to them now. You may increase or decrease each stat by 50%, but must have the same total you started with and cannot have an average change (absolute value) more than 25%. Now you may apply special traits, all of which have a point value.

Speciality points:
Throughout, there are some options that cost speciality points. These options are inherently superior to the others, but have a value assigned to them. You have a set number of speciality points you can use, and cannot exceed it. However, not all options cost speciality points. Specialities and speciality-costing parts provide larger bonuses for smaller creatures, so smaller creatures get stronger special abilities in exchange for the disadvantage of small size. Make sure you spend every speciality point, there's no benefit in leaving them unspent and there are many 1pt features and parts you can use. An example of a special feature would be health regeneration (1-9pts), which increases health recovery. An example of a special part would be a detox organ (1pt) that detects poisons once they reach a certain dose and reacts to them, shortening duration and increasing dispersion rate, while also providing a greater resistance to poison of that type not yet absorbed.

Character grade:
Some creatures are inherently superior to others. These creatures get more speciality points than others, higher derived stats than others, and so forth. This is referred to as character grade. By default, player species are of the "normal" character grade. Most wild animals are of the "inferior" character grade, and very weak animals are of the "nuisance" character grade. Only very rarely is a creature "superior" or above. The grades are listed below.

Nuisance: 50 speciality points, 1x integrity, 2x health, 4x stamina, 8x will, 50% progression, 125% regression. Four per player party slot.
Inferior: 75 speciality points, 1.5x integrity, 3x health, 6x stamina, 12x will, 75% progression, 112.5% regression. Two per player party slot.
Normal: 100 speciality points, 2x integrity, 4x health, 8x stamina, 16x will, 100% progression, 100% regression. Takes one player party slot.
Superior: 125 speciality points, 2.5x integrity, 5x health, 10x stamina, 20x will, 125% progression, 87.5% regression. Takes two player party slots.
Divine: 150 speciality points, 3x integrity, 6x health, 12x stamina, 24x will, 150% progression, 75% regression. Takes three player party slots.
Deity: 175 speciality points, 3.5x integrity, 7x health, 14x stamina, 28x will, 175% progression, 62.5% regression. Takes four player party slots.
God: 200 speciality points, 4x integrity, 8x health, 16x stamina, 32x will, 200% progression, 50% regression. Takes five player party slots.