Toward the end of a session in Stellaris, your empire is likely quite advanced, powerful and hopefully a major player in the galaxy. But in this final act, the game will also give your empire the ultimate test of survival. An endgame crisis is an event that threatens the entire galaxy, with each having an express purpose of destroying all forms of life.
These galactic invaders won't accept any sort of diplomacy or even surrender, meaning that either you succeed in stopping and destroying them, or they wipe out every empire in the galaxy. While this can only occur once during each game session, they are powerful and terrifying to face. A crisis' strength setting determines the stats of each of its ships as well as their weapons damage, scaling from 0.25× to 25.0×. Higher difficulties will also make every crisis more powerful.
Thankfully, because they are so powerful, you'll find many other empires are willing to put aside their differences to fight these galactic invaders. Even some Fallen Empires will awaken and become powerful guardians. Additionally, you can choose an ascension perk called Defender of the Galaxy, which provides a 50 percent damage boost for your fleets whenever they fight a crisis fleet. Still, with how powerful all these invaders are, you'll need all the help you can get, so let's go over each crisis that can appear and how to counter each of them.
Prethoryn Scourge
The Prethoryn Scourge is the base crisis, triggering if the other crisis events aren't met. Starting off as a warning of distant echoes in the space outside of your galaxy, you'll be made aware of a huge swarm coming towards the outer rim. Roughly five star systems will be marked as the initial site of the invasion, at which point the Scourge's vanguard force will arrive. The main invasion force will follow a few months afterwards. From there, the Scourge will begin infecting planets wherever they can, with colony ships used on uninhabited worlds and transport ships invading an empire's colonies.
A massive hivemind, the Prethoryn Scourge make use of organic ships with lots of armor and weapons such as strike craft, missiles and acid bursts. Since they don't use shields, equip your fleets with energy weapons that can deal extra damage to armor and hull. Remember to salvage from Prethoryn ships, as their own weapons are quite effective against them. Empires which lack the numbers or power to fight the Scourge directly should focus on containing their expansion. A good strategy might be to have lots of smaller, nimble fleets composed of corvettes and destroyers to hunt down their civilian equivalent ships.
If the Prethoryn have conquered at least 20 percent of the galaxy, a friendly empire called the Sentinel Order will spawn. They are a military order made up of species from different empires that fell to the Scourge and are willing to help nearly all empires as they fight the swarm. They posses Fallen Empire equivalent technology and weapons, and they are willing to loan some of their ships to empires that have been successful in fighting the swarm. After the Prethoryns have been destroyed, the Sentinel Order will be disbanded, and their home system will be up for claim.
Contingency
This crisis has a chance of spawning if any empire has researched synthetic technology and has a large mechanical population. It begins with an event called the ghost signal in which synthetic pops from every empire gradually go missing. This ends with a message that the Contingency has been activated.
From there, four random star systems with uninhabitable planets will be transformed into machine worlds called sterilization hubs, along with a defense station and robotic fleets. Like all other crises, diplomacy is impossible even if your empire consists of a machine race. The ghost signal will affect any mechanical pops and ships equipped with the Sapient Combat Computer, with its strength measured in five levels and starting at five. Thankfully, every time a hub is destroyed, the signal gets weaker.
Contingency warforms use a blend of strong shields and armor. However, they have very weak hulls, so weapons focused on penetrating these defenses will most effective. Additionally, your fleets should focus on equipping lots of shield defenses against their energy weapons. Once all sterilization hubs have been destroyed, a fifth and final system containing the Contingency Core will spawn. When this happens, prioritize destroying this final sterilization world, as it will result in the Contingency and all of its forces deactivating regardless of what battles, events or projects are underway.
If the Contingency have conquered up to 20 percent of the galaxy, the Cybrex empire will spawn. Originally a precursor empire, the Cybrex will resurface from hiding to fight the Contingency, and will leave the galaxy after the crisis has ended. They function almost identical to the Sentinel Order, meaning they will occasionally provide a fleet to empires that are successful against the Contingency.
Unbidden
Unlike the other two, which provide warning several years in advance, the Unbidden's arrival can come without warning, with a dimensional portal opening in literally any random star system of your galaxy. If it spawns within an empire's borders, the local starbase is instantly destroyed. From here on, fleets will continually spawn from the portal. Their construction ships will begin building starbases in any conquered systems. While they don't have transport ships to invade colony worlds, their fleets will instead simply bombard the planet until reaching 100 percent devastation, turning it into an uninhabitable tomb world.
When the Unbidden cover at least 15 percent of the galaxy, a second (and later a third) extradimensional portal will spawn, bringing forth the Aberrant and the Vehement respectively. While all three of these factions are hostile to the galaxy's empires, they are also hostile towards each other. This can be a mixed blessing depending on the situation. On one hand, their arrival can mean that you'll have to fight a war on two fronts, but on the other, with the invaders fighting each other, it allows you to destroy their starbases and anchors while they are distracted.
The invaders' fleets use only shielding defense, and can be effectively countered by making sure your own ships are equipped with kinetic weapons that can quickly bring down shields. You can also research their technology. However, their weapons are meant to destroy armor which they themselves don't use, so refitting your ships with their weapons is not advised. Each starbase owned by the Unbidden acts as an anchor that keeps the main portal open, so before you can think about destroying the portal, you'll first have to destroy all their starbases.