If you find any events in the game that further prove, contradict, or suggest an entirely different outcome, please don't hesitate to post.
Despite extremely unlikely odds, the rebel flagship was defeated by a decommissioned federation ship hastily fixed for battle called 'The Kestrel'. The rebels was chased down, their power heavily deminished and ensuring a federation victory! Unfortunately, the war brought with it many tragedies. The rebel fleet destroyed many areas of the galaxy and many were forced to leave these places. Many soldiers and pirates were killed from both sides and the federation is still in disarray and in even more debt then before. The rebelion, while much weaker, still prospers in many influenced sectors.
New Alien Races
Two new alien races were discovered:
The Crystalmen may look very similar to the rockmen but are in fact very different culture wise. They left the rockmen many millennia ago due to disagreements with their culture. Thus the race constructed a portal to a far away section of the galaxy where no rockmen can find them and deactivated it, blocking contact with other races. However, even after many millennia, the rockmen never dismantled the portal, long awaiting the crystalmen to come back.
When the portal was reactivated by a crystalman called 'Ruwen' and the Kestrel went through it they were instantley caught and the news spread faster then wildfire among the crystalmen race. Thoughts were mixed throughout the community. Some saw this as a once in a thousand lifetime chance to get their hands on the artifacts of other races. Others were openly racist to the crew of the kestrel and tried to get rid of them, preferring the isolation. Many were just scared for the new alien species and rebellion fleet trying to kill them. Depsite all this the crystalmen always knew of the existence of other aliens due to the portal.
The crystalmen were a surprisingly technological race, so contact was made soon enough and the 'Tektite' was offered to the Federation as a part of the diplomatic discussions. This brought the invention of many new technologies, which we will get to later.
My view of the history between the Rockmen and Crystalmen
How I see the crystalmen is that thousands of years before the events of FTL the crystalmen and rockmen were all the same species, which it was I don't know so I will just call this ancient race the mineralmen. There were two main cultures, The brutish culture which was centred around brute force and honour - which would become the rockmen culture - and the enlightened culture about peace, enlightenment and technological development - which would become the crystalmen culture. The mineralmen needed both cultures to keep balance amoung the people, but while those of the brutish culture didn't mind the prescence of the enlightened culture, this was unfortunately not the same for members of the enlightened culture. They eventually had enough, built a portal far away and then deactivated it, ceasing contact with the brutish culture and they eventually prospered and evolved into the crystalmen.
For the brutish culture however, this sudden removal of the intelligent in the mineralmen race eventually led to the halt of technological development for those left behind, along with a government crisis as all members of the mineralmen government at the time followed, for obvious reasons, the enlightened culture. Eventually the government was taken over and propaganda spread among the rock people, promoting the idea that other cultures are wrong, evil and must be destroyed from the universe. However, the government knew they couldn't survive without the itelligence of the enlightened culture, so despite the views of their propaganda, they kept the portal to the crystalmen homeworlds in the hopes that they would come back, which they never did. This culture eventually evolved into the rockmen.
The Lanius (Lanii?)
The Lanius are a scavenging species that absorb sources of scrap metal for nutrients. They can hibernate for many centuries to conserve energy to survive and only wake when they detect a large supply of scrap metal, like a giant ship-yard worth of destroyed ships. This lead to the Lanius congregating around former-battle fields and sectors destroyed by the previous rebel fleet. Their level of hostility can vary wildly. Some only scavenge the wrecks of already destroyed ships, staying away from ships containing sentient lifeforms because, according to some friendly Lanius, of a rule, suggesting some form of government or religion. Other Lanius, however, seem to ignore these rules, suggesting anarchy across the race. Even so, as a whole, they seem somewhat friendly towards the federation and Lanius store owners seems to not mind selling to non-Lanius. Despite the friendliness of some Lanius (An exact percentage would be great) abandoned sectors have been labeled 'hostile' and the Federation is setting up research stations to study the Lanius. Some evidence suggests that the Lanius did know about other sentient lifeforms before and have been in contact, with there being loosely followed rules stating that Lanius can not absorb the metal of other lifeforms.
The surge of technology
With the discovery of new species, both of which have more advanced technology, and the halt of the war the galaxy can now somewhat invest some time and money into new technology.
Many new weapons were made, most of which charge and chain weapons but a new type of weapon called the flak were found to be used by the Lanius and now by the Federation. The flak consists of a container filled with scrap metal and a projecting device which allows the scrap metal to fling itself to enemy ships quickly enough to cause some damage. Why do I think it was invented by the Lanius? Well because its projectile is bits of scrap metal, which the Lanius would likely have an abundance of to make into a weapon.
Systems, oh so many new systems to choose from!
First of we got mind control, most likely invented by slugs then stolen by the Federation. Why do I think mind control was made by slugs? Because I highly doubt a government like the Federation would invest much money into a system that gets rid of free will, partly for ethical reasons and mostly so the Federation's few allies don't leave.
Then we go into hacking, which allows to disable any system for up to 10 seconds. This really could've been made by anyone but from process of elimination its probably the Lanius:
Reason 1. The federation is in crippling debt and struggle, highly doubt they'll want to spend time and money to help invent a whole new system.
Reason 2. The Engi type C cruiser states that, 'The Engi were quick to adapt to the sudden surge of hacking technology - this ship is the result of their research.' It says the engi adapted to the technology, suggesting that they did not invent it.
Reason 3. The hacking drone consists of a huge drone hurtling towards the ship. Why isn't the hacking system just a giant computer that can just hack into the enemy's reactor and disable all systems, probably because it was invented by the Lanius, likely the least advanced species in the galaxy technology wise.
And we get into the question of immortality itself, removing all purpose to life and probably causes much debate and protests, the clone bay. Who invented this process, to be honest it could've been many species but I reckon it was the crystalmen. From what we see of their technology we know that they are very advanced technology-wise, they have a statis pod that can resurrect a broken crystalmen, which is pretty close to cloning, and they built a teleporter, a giant teleporter that can transport not only one ship but a whole rebellion fleet! All this and that teleporter was activated by a single crystalmen. If any species is capable of making a system that provides immortality, its them.
Last, and certainly least, we got the back-up battery. There isn't really much evidence to suggest who invents this. I have my suspicions on the zoltan, due to its presence on the Cerenkov, but they don't really have a need for this since their body is a giant back-up battery.
The Constriction of Flagship Mark II
Under the nose of the Federation, the rebels were hard at work constructing a new flagship in their newly set up stronghold. The rebels were also quick to adapt to the new technology, implementing the new systems and drones into the flagship. The rebels would also construct a line of ships incorporating the new systems, most notable the clonebay which was now seemingly replacing the medbay on every modern ship (Every type C cruiser has a medbay.) The rebels also took into account the strategy used by the Kestrel in the first war, so they decided to connect the laser and missile artillery rooms (Only on hard mode). When the flagship was done the rebels restored their sectors and prepared the rebel fleet again.
Eventually long-range sensors/Federation spies/Engi stealth ships/*insert method here* found out about the new fleet with new systems, notifying the Federation and preparing a last stand like the previous war. And later, long-range sensors/Federation spies/Engi stealth ships/*insert method here* found out about the flagship construction, sending you to deliver that information. However, long-range sensors/Federation spies/Engi stealth ships/*insert method here* could not find out about the rebel's construction of a second flagship. Luckily, the Kestrel found this 2nd flagship mid-construction in the rebel stronghold, along with a Federation Cruiser.
John Luke Pack Hard wrote:The Perpetual Player - History Repeats Itself
The captain of the "Kestrel", whose name was never recorded, leads his small, hopeless craft to the Federation core sector. Although s/he gathers plenty of resources and upgrade the ship to become rather formidable, most of the time a string of bad luck or careless decisions would lead to his/her demise. That or the rebel flagship, upon seeing "the last hope of the Federation", would enjoy a good laugh, and then blow the "Kestrel" to smithereens. Most of the time, the captain decided against taking the Kestrel and using a more powerful ship supplied by over-space manufacturers. That only resulted in a different ship being blown to smithereens. They also didn't come with warranties. How sad ;(
At some point a technician had to come and reboot the universe, because the "retry" button can only bend time up to seven times.
Eventually, the captain leads a vessel armed with legitimately acquired and totally not modded weapons and destroys the rebel flagship, scattering Rebel command and resulting in Federation victory over the Rebel fleet.