Context: in most continuities Megatron starts the war due to the autobots basically owning a slave laborer class that lives and dies mining energon(one of them being megatron) or fighting to the death for entertainment megatron then starts an uprising and creates the decepticons to free his fellow workers and gain independence but along the way his message gets corrupted and megatron becomes the warlord tyrant he fought so hard to tear down(so the once noble faction becomes the bad guy decepticons we know and love today)
The guy who got away at the end is JetFire. In the g1 cartoon he and Star Scream had a little bit of different history and he was also that flying autobot who showed up in the first chapter of the autobot campaign. Also yeah this game is pretty gray and dull visually sometimes though there are some stand out locations. Won’t spoil too much but I will say chapter 3 in the deception campaign is a pretty neat environment.
for why a lot of bots are cars and why megatron is doing all this: the alt-mode a cybertronian can transform into is part of them as soon as they're built/born (formed out of the planet like liquid metal) and in this universe it was nearly impossible to change from one type of altmode to another without insanely extensive surgery. if you're a car guy you can be plenty of cars but you're not being a jet anytime soon. before the war, cybertron was ruled by a caste system where your alt mode determined your job permanently. it was pretty bad so orion pax and megatron, two best friends, tried to change it. megatron wanted violent revolution while pax wanted reform the council agreed to change with reform and appointed pax as the new prime, optimus prime (he chose to just call himself optimus as he believed himself unworthy) and megatron saw this as a giant betrayal. kickstarting the full autobot decepticon war as megatron slowly went more and more insane and power hungry that all leads to this game, where megatron is now using the power of dark energon (essentially the blood of space-satan) to become stronger, you'll see what optimus has to do to counter this later on in the game
To not spoil too much, but help you have a basic understanding- Yes, they're pure machine. They have a "spark" in their chest, and also run off of Energon. To put it simply(someone correct me if I'm wrong): Spark=Heart, Energon=Blood. And I *think* that yeah, the Autobot/Deception thing is basically a political party sorta deal. There've been people on both teams who have changed sides(Like Sentinel Prime in DotM- F*** you, Sentinel, I'll never forgive you for Ironhide)
Fun fact, Steve Blum voices arguably the most vile being in this game. The first game is more or less narrated as a retelling of the events by Shockwave, who puts every single maniacal scientist to utter and absolute shame with the most horrific and inhumane (well, as humane as it gets for robots who can transform, which arguably could make it worse, all things considered) experiments that he does to EVERYTHING he can get his hands on. Even if Megatron isn't robot Jesus, Shockwave is 100% BEYOND robot Satan. And also Barricade, so I felt it was required for me to play him at LEAST once XD
I’ve always said that War is a better GAME than Fall of Cybertron. The latter may have better/bigger and more epic set pieces, but as a fun product with more going on and more enjoyable gameplay, War is the better game for me, personally.
Yes, they have organs, the most important ones are the spark (heart and soul), the processor/neural cortex (brain) and T-cog (the organ that lets them transform), they also are all cybertronians so being an autobot or decepcticon is a choice, there's other factions like the mercenaries, maximals and predacons (basically an evolution of the autobots and decepticons that transform in animals), however there's some transformers that were technically born autobots or decepticons, but that's only because they were built during the war, which leads me to the question of "are they built or born", the answer is both, how they are born however depends on the continuity, sometimes they just split from an already existing transformer like a cell, or they emerge from the ground of Cybertron. Most transformers can only transform in certain things like cars because of their body type and size, so a cybertronian with a jet body type will always transform in any kind of jet that they want, and the same applies to cars, bikes and other vehicles, they can change their body type but they need to basically make a new body at that point, there's some cybertronians that don't have this problem because they can have more than one alt mode but they are pretty rare.
Also to describe the Autobots, they’re like militaristic space hippies with some elements like labor unions/other cells while the Decepticons are kinda like a mix of Reign of Terror French Rev but also with elements mixed in from dictatorships under figures like a certain mustache guy and Stalin
Quick lore dump: Most things on their world that are alive have a spark that gives them a soul of sorts to either reincarnate switch bodies. So anything without one is a drone or just a regular machine. A for life span they can live for thousands if not millions of years. BUT without energon they starve rust and die out like a human would without food in a matter of months. Hope this helps!