Just coz you won't be able to build the ships in the main game, doesn't mean you won't be able to mod it so you can. 
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I'm the guy writing the random events, and on the "alien encounter" side of things, so far i've got:
The Borg
They assimilate systems, initially invading with small scout ships and moving up to Spheres, Cubes and eventually even the Diamond. If you take out the Diamond, they will stop invading you for a time, but they will continue to spread from the Delta Quadrant. The only way to completely destroy them is to wipe out their systems.
The Sphere Builders
The Sphere builders slowly make the space around them uninhabitable, causing the inhabitants in nearby systems to die. You need to reach a certain tech level before your ships can take out the Spheres in combat
Species 8472
They pour out of a fluidic gate and destroy everything within sight - including Planets themselves. You have to fight them to stop the invasion. Individual Bioships are relatively weak, but their weapons and shields recharge at an extremely high rate. They also attack en-masse, so it won't be easy to defeat them...
Chodak
Same as BOTF, it appears without warning in a random sector, you fight it.
Giant Amoeba
You fight it. It attacks ships by "eating" them. If you manage to scan it AND defeat it, you will get a large Biotech bonus. If it enters a system, it will begin to wipe out the population until it or the colony is destroyed. It will then move onto another system and begin destroying it if it is left alone.
Gomtuu
One-time all-round research bonus if you can scan it AND survive the encounter. Ships will need POWERFUL shields to survive the initial attack. If you hail it and survive without attacking it, Gomtuu will cease to attack you and will instead attack your enemies until they manage to destroy it.
Jellyfish from TNG Ep. 1/2
Doesn't attack your ships. It will instead attempt to escape as quickly as possible. If you manage to scan it before it escapes, you will get an energy and/or contruction tech bonus. You will get no bonus for destroying it.
Crystaline Entity
Same as BOTF, you fight it. If it enters a system, it will begin to wipe out the population until it or the colony is destroyed. If the colony is destroyed, it will then move onto another system if it is left alone. However, if you kill it, you will suffer from a small Empire-wide morale drop.
Doomsday Machine
If the Doomsday device enters a system, it will destroy one Planet every turn. It attacks ships by ramming into them, and you will have to battle it to destroy it. The Doomsday machine will have many thousands of hit points, but no shields. (It's made of Neutronium afterall, it doesn't need shields!)
Husnock
Same as BOTF, it appears without warning in a random sector, you fight it. Ships that survive the battle get an experience bonus for fighting this unusual enemy.
Calamarain
Same as BOTF, it appears without warning in a random sector, you fight it. Ships that survive the battle get an experience bonus for fighting this unusual enemy.
The Echo Papa 607 Defence System
Similar to BOTF, but can only be found in the Minosian system. You get a weapons tech research bonus by scanning it AND defeating it, and ships that survive the battle get a large experience bonus for fighting this unusual enemy.
Cytoplasmic being/void
Acts like a gigantic Echo Papa 607, but you get a biotech research bonus by scanning it AND defeating it. Ships that survive the battle get an experience bonus for fighting this unusual enemy.
V'Ger
(Not sure yet)
Q
A ship is thrown to a random sector. The ship will have to attempt to make it back under its' own fuel reserves, so making alliances with the locals will be essential. Greatly increases the chances of contact with the Borg, irrelevant of where in the Galaxy the ship is sent.
Caretaker array
A random ship is sent to the Ocampa system in the Delta Quadrant. Contact with the Ocampans is impossible until the Caretaker is destroyed, but the Ocampans will be defenseless and prone too attack if you do this. The Caretaker is a bit weaker than the Edo Guardian.
Think-Tank Ship
Once discovered, you recieve a one-time only ten turns of 50% Research Empire-wide in exchange for a random amount of resources.
Voth City Ship
One ship in the encountering fleet is captured by the Voth. It will be returned 20–50 turns later with a large all-round research bonus.
Krenim ship
If it appears in a system, the system and all nearby surrounding systems will undergo shifts, resulting in different planet types, populations and system bonuses.
Pralorian Androids
Only encounterable in the Delta Quadrant, Pralorian Android ships fight their own private battle – and may attack inhabited systems arbitrarily until destroyed.
Promellian Battlecruiser
May be found afloat in Nebulas. If you scan the ship, you will recieve a 4 turn 100% research bonus in a random field.
Of course, these are ALL subject to changes, additions, or even removal from the game. I have written every event that I could possibly think of, with help from Dafedz and OmniQ, but this does NOT mean they will make it into the game. It will ultimately be up to Jigalypuff to decide which ones to include/are programmable.
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when we meet them. Its far cannon like this than just eridicate them. And that option will be available as soon as you reach level 10 or higer on Computer Reaserch.
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