The concept of a Great Filter is similar to stages of a user's bot development as, there are several steps most users go though in development that allow their bot to thrive on a server. Though you could think of these as 'goals' to complete, Screeps is ultimately a sandbox game, meaning you can do as much or as little, as you want. However, if your talking in terms of survival of a colony of creeps there are repeatable patterns that emerge in development that almost all bots follow or have some aspect of.
Creep Management - Roles, States & Tasks/Goals
The first step is to have one creep take an action, however, a user inputting multiple actions one a creep manually is not effective as a colony grows even a little. A user and subsequently their bot, needs to beable to have creeps do tasks automatically based on the conditions of their environment. There are several methods for this, and the ones listed here are by no means 'the only way'. It is up to the user, how to structure their bot.
The tutorial for Screeps presents a solution in roles, where each creep is assigned a role and based on that role they have logic to do actions based on their environment. Roles can be made to fit almost any situation, but the creeps who do them often are 'locked' into their specific role unless logic specifies elsewise, meaning at base, if a creep has completed its task and there are no more tasks for it to do, unless the user specifics something more/new for it to do, it will sit until conditions change in that it can act again.
Another type of of creep management is generic creeps, in where a creep's body is formatted to be useful for several tasks and the creep is assigned a task/goal based on a colony's needs, stresses or environmental conditions. In this way, an individual creep only needs to worry about the task/goal it was assigned and take actions accordingly, but can also when done be assigned a new task/goal. This does make creeps more dynamic, however, as their bodies are often suited for multiple tasks, the tend to be bigger/more energy expensive depending on user setup, then a specific role creep who does one thing.
As creeps only have a limited life-span, the next filter is making sure a colony is maintained with new creeps, when the old ones die of old age or other factors without direct user intervention. And if the worse happens and a colony is wiped out, the spawning system needs to beable to re-start itself.
The tutorial sets up a way to do this in the form of a 'headcount', every tick creeps are tallied up and check against hard-set values in a flowing else/if condition setup. If during the execution of the else/ifs a condition is met and/or fails (depending on setup) then the spawn is told to spawn a creep to replace the deficit. This can be evolved upon to be more dynamic as a user refactors their code.
Another method of spawning creeps is with a queue, meaning that a user's code looks at conditions as they are in a colony and pushes an element to a 'queue' for the spawner to take care of in order of importance/receiving. Then, as it gets entries, the spawner handles the queue as needed.
If it is a invader or another user, at some point a colony will be attacked and need to defend itself. Invaders will show up eventually in almost every case for a room and will only get more frequent as a user gets more efficient at mining energy. While they do not kill spawns directly, they can easily break pre-set spawning code by killing off the total creeps of a colony. This makes defending from them in a timely matter not only a time-saver in respawning lost creeps, but vital for survival. Users will rarely stop at killing creeps however and, if your spawn is undefended and they go uncontested, it could easily end up in you needing to respawn. Invaders are the first stage to get you going on defense, but ultimately you will require more to keep other creep colonies from wiping you out.
You can read more about defense here in screep's official docs.
Proxy Harvesting & Excess Energy
While one room can provide sufficient energy to get started, effectively going to nearby rooms, harvesting their energy and bringing it back for the colony enables faster development as you can pump more energy into upgrading your controller, spawn more creeps/spawn them faster, and keep energy stored for times when you need it. This is known as proxy harvesting.
Getting a creep to their designated room, then to the source and mining the energy is the first step.
Getting a creep to return with their harvested energy, or assigning creeps to bring that energy back is the next step.
While not strictly required, reserving a room allows more energy to be harvested from the room and to keep other's from harvesting it.
A colony needs rooms to grow and harvest from, occasionally those rooms are occupied by other users' colonies. Mounting an offense to take/capture rooms from other users helps a colony expand further.
Using the screep's market enables players to not only sell excess resources they have acquired, but purchase from other users as well. This enables more energy to be brought into a colony in a very short time, or resources that help boost other things that a colony may not beable to make/farm on its own, such as power, deposits, or boosts. Making this automatic, is a great step in being able to bring in more items to help the colony thrive.
Lab logic & Boosts
Another filter that tends to happen late in a colony's development is the implementation of labs to create compounds and boosts, and then in turn use those boosts to enhance creep's abilities. While not strictly 'required', another user can easily overpower a user's creeps / defense using boost and the only real counter is to use boosts in-turn to make up the gap in power. Lab logic can get complex/expensive and, boost logic can be challenging, but automating and/or mostly automating the process goes a long way in boosting a colony's defenseive/offensive/harvesting power.
While this can be some-what circumvented with the use of the market, being able to find and then subsequently harvest valuable resources on the highways such as power and deposits helps a colony gain power and credits.
Source-keepers guard very valuable rooms that can help boost a colony's energy and mineral input. There are several tasks to overcome when Source Keeper Mining, such as dealing with the source-keeprs and the powerful raid invasions that happen when an invasion is triggered.
Inter-sharding (when shards exist)
Intersharding can be a big step in enabling multi-shard buying/selling of resources, and allows for a user's colony to find more rooms available to them if they run into neighbors they can't/do not want to remove.