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If you study how to co-exist with them, it will tell you why they attack your ships so I'll let you figure that out for yourself.
They travel in packs and have a sort of size-like hierarchy. Each big amoeba can spawn a little fleet of smaller attack organisms that act like fighter strike craft. Later in the game, you can incorporate those organisms into your own ships and send little swarms of amoeboid allies to attack enemy vessels. You can also eventually incorporate their cellular regeneration powers into the hulls of your own vessels.
There is an event in which you discover an infant amoeba which you can nurture and which will then become a ship you can command like any other. If you can keep it alive for a century, it will grow into a very large creature indeed. There are also origins and civics that let you reanimate dead amoebae, so you can have undead amoebae in your fleet.
If you don't learn to coexist with the amoebae, they're a minor impediment to your initial expansion. They cannot destroy a starbase outpost, though they can temporarily neutralize it if it is poorly defended. Amor Alveo is a tough fight, but the wandering packs of ameobae can usually be taken out with one or two fleets of corvettes.
If they're blocking your construction vessels or your science vessels, you can set the vessels from "evasive" to "passive" on the ship command menu, which means they will no longer run from threats. The amoebae will only attack if your vessels move too close. So I wouldn't recommend trying to survey a system with an active amoeba in it, but you can usually steer your ship past them safely if you do the steering yourself and want to see what lies beyond the system they are active in. They do migrate from system to system, so they may appear in space you thought was clear but that also means they may disappear from space you thought was blocked.
choose battles carefully.
literally the plot of Marathon lmao
oh, i havent been able to see wath is in the tau ceti system since my intel over there is basicaly non existent and everytime i send anything there it dies to said hostile fleets!
Edit: its automated mineing drones how do i deal with them?
Most of the time, the drones will be weak enough you can defeat them easily with a fleet of 20 corvettes. Technically you can do it with half that. They have no shields and only use lasers, so if you want to tailor a fleet to counter them, give your ships shields and lasers. But with sufficient firepower, a balanced fleet can easily do the job.
Early in the expansion phase, mining drones can be a bit of a mixed blessing. On the one hand, they block your advance. On the other hand, they block the advance of whatever is on the far side of them too. So sometimes that means they're blocking a pocket of systems you can wait and come back for later after you've joined frontiers with other powers. Other times it means they're holding back an aggressive enemy who will require more attention to deal with than the drones do.
So, in general, they're a problem that has to be dealt with by force, but because they won't move from the system you find them in, you don't have to rush to deal with them. You have all the technology and potential firepower you need to deal with the average drone fleet from day one of the game - but I'd recommend waiting until you've built your first 20 corvettes unless you're in a real hurry for some reason.
It will slow down your expansion, but signing a non-aggression pact, or even a defensive pact, will give you some assurance that you won't face an immediate threat from that direction. Once you have a border with a neighbor you need to start looking to your defense, and especially when you're new that's easiest done by looking to other neighbors for allies.
So my classic mop-up crew used to be corvettes with only plasma guns. Shields are better defense against mining drones, while the amoeba have strike craft (ignore shields).
Crystals are generally too strong to kill early on.
Just make sure to refit the corvettes to auto-cannons and laser once you have to fight other empires, or just to impress the AI with high fleet power.
And yes of course the pacification is great. This also spawns more amoebae / crystal fleets within your borders, fleet power in the thousands. They also should attack everything hostile to you, wether it is pirates, meteors and whatnot.
If you have neither option, disable the evasive mode on your science ships, fly through the hostile system, re-enable evasive mode and keep surveying beyond.
With amoebae patrols, make sure to move several systems because the evasive mode lets the ship return to where it came from (killing the ship if the amoebae hunters catch up)
but yeah were doing good with my neighburg and theire quite big + theire like super frendly and really nice to me.
A basic good rule for early on is that your first friends are your friends because they're close. Later you will be able to pick friends because you get along well with them. So it's often a good idea to make good friends even with bad neighbors. Then later when the Galactic Community forms, there will be a chance for people to team up with more like-minded friends and those first alliances of desperate convenience tend to come apart.