The endgame content in SCZ is:
Neural Simulation (a.k.a. "NS")
This is a permanently available mode, found under Fight -> Dispatch -> Neural Simulation
Supreme Battleground (I'll sometimes refer to this as "SupBat")
This mode is only available during certain events, although these days it tends to appear in every event.
These are really the only "endgame" content in SCZ because they are the only game modes where an experienced player will need to use skill, powerful operatives, and good teambuilding in order to get the best reward[s].
Whilst much of the rest of the game may seem difficult to a new player, to an experienced player no other content provides much challenge or requires teambuilding.
For all other content in the game, you can use a 4* like Wednesday with the free 4* weapon the game gives you (Work-in-Progress) and she'll generally be able to clear all content in the game. She won't have the damage or clearspeed of a 5* operative, but she can do it.
Stronger 5* operatives that have some investment into them will easily destroy all content other than Neural Sim and Supreme Battleground.
Both Neural Sim and Supreme Battleground play largely the same:
There are two bosses, fought separately
You have a team of three operatives for each boss
Your best clear time is recorded for each boss (this is the "Best Evaluation Record")
You are also given a "score" for each boss, but that's literally equivalent to the time taken to beat them.
The operatives used for one bosses Best Evaluation Record can't be used for the other boss
You can do a boss again with different operatives, and then overwrite the Best Evaluation Record to free up those operatives so you can use them for each boss.
Each week, each Neural Sim boss will gain +25% resistance to one damage type.
Which type is random, but the two bosses won't ever have the same +25% resistance.
Each week, each Supreme Battleground boss will gain an effect that gives +30% resistance to two damage types and 30% weakness to two damage types
Which specific effect a boss gets is random, but both bosses won't ever get the same effect.`
Each boss gains a +resistance modifier each week, but the +resistance mods the bosses get can't be the same.
Whilst many bosses do naturally have a high resistance to some damage types, the chances of one boss naturally having a high resistance to one damage type and the other boss gaining a +resistance modifier to that damage type is extremely low.
If you invest into one main DPS operative, then they'll likely very very good against at last one of the bosses that week, so you can use that DPS operative against whichever boss they are best against that week, and get a very good score with them.
You can then use whichever other operative you have that works best against the other boss, and hopefully get a decent score - with enough operatives you'll likely have an operative that works well against them and can get a good score just because of how well suited they are, even if they have little investment.
This generally allows you to focus on one main DPS operative and 1-2 supports, thus getting a very strong team very quickly, whilst also getting good scores.
Alternatively, you can focus on two main DPS operatives - generally speaking you should almost always have each operative be capable against one of the bosses, allowing them both to get decent scores.
Since many support operatives work well without much investment, and many support operatives gain a lot from their earlier manifestations, this allows you to get two teams that can get good scores quite quickly.
Further note that since both Neural Sim and Supreme Battleground involve fighting one boss at a time, single-target damage is generally all that matters for endgame.
AoE damage is nice to have and useful elsewhere, but having more of it in endgame content doesn't really help you get any extra rewards.
I.e. For all non-endgame content, slowly clearing enemies one-by-one with a single-target character gets you the same rewards as quickly clearing entire groups with a super-powerful AoE character. Neural Sim and Supreme Battleground are really the only content where this isn't the case.
In NS you get 10,000 points for actually defeating the boss, regardless of how long it takes you.
For each 0.1 seconds under 300 seconds it takes you, gain an extra 10 points.
(Equivalently, gain 100 points per second under 300 seconds it takes you.)
For a KillTime in seconds, the formula for your Neural Sim score is thus:
10,000 + ((300-Kill time)*100)
As such, the theoretical maximum score for a Neural Simulation boss is 40,000, which you would get if you killed the boss instantaneously, although that's impossible in practice.
Many bosses have mandatory invuln phases that mean there are limitations to how fast they can be killed, and as such what a "perfect" or even "good" score is will be different for each boss.
Similarly, many bosses can take longer than others due to things like:
Having lots of HP
Not having any major weaknesses to any damage types
Certain mechanics that make them more difficult to hit or damage (e.g. teleports)
Dealing lots of damage to the player, potentially forcing you to stop dealing damage to move out of the way of attack
Whilst each person has their own definition of what they consider good, I'd say that, generally speaking, any score over 30,000 is respectable, and anything over 35,000 is very good