I've got someone helping me with the storyline, so here's what he's come up with so far.
Backstory:
Long ago, during the time known as the information age, humanity attempted to grow closer together in the bonds of friendship. However as the earth's dwindling supply of non-renewable fuels and energy sources, the nations of the world fought amongst themselves to gain the last remaining sources of energy to keep their electricity-driven economies going.
By 2050AD, despite desperate attempts to seek a replacement of the old energy sources, the world was on the brink of an energy crisis. The more desperate people grew, the more they put aside their differences to work to solve their common problem. Finally, there was hope. A UN special task force was able to put together a viable alternative fuel source; if a massive shaft could be drilled into the planet's molten innards, the resulting heat released could be harnessed into energy enough to power the earth fifteen times over.
The nations of the world came together in a new spirit of co-operation, powered by desperation and the spectre of doom should they fail. Having expended the very last fossil fuel reserves on earth to do so, the massive thermal bore began operation in 2061, and once again, there was enough energy for all.
However, as the energy crisis faded, the need for co-operation faded as well, and humans began to fight amongst themselves once again. As the conflicts once again intensified, the nations made one last agreement: No one nation would be able to destroy humanity's lifeblood: the bore would be kept as neutral ground, and to ensure it stayed that way, a fortress was built over it, one maintained not by humans, but by machines.
The fortress was built around a massive automated defence AI, known as "godfather", it controlled the thermal bore and all of it's facilities. This central computer was given it's own production facilities, and ordered to protect the borehole. Over the years, Godfather built a huge ring of defences around the central complex and the borehole. The entire structure became so big, that Godfather and the humans simply began referring to it as "the city".
As the years passed, many attempts were made by the huamns to conquer the borehole and the city over it, all of them failed, but Godfather began to notice a disturbing trend; the human weapons were advancing, growing in effectiveness with every attack. Godfather attempted to develop new weapons of his own, but found that the combined duties of defending the city, controlling production and developing new weaponry was too much for even his formidable computing power.
Godfather came up with a solution quickly. He constructed two copies of himself, in smaller bodies; Lectro, the ultimate fighting android, to defend the city, Sxulls, to develop more effective weapons and defences and Grlmm, specializing in appropriating raw materials and turning them into new members of a growing android defence force, patterned after creatures of human myth.
For many years, this new arrangement worked well, damage from human assaults on the city was reduced to a minimum, until one day...
The power cut out...
Game Story:
Prologue: Turbine Complex
This stage serves as a tutorial, Lectro starts with all of his weapons. Lectro is ordered by Godfather to find the source of the power outage by descending into the bowels of the city and into the borehole. After learning basic movement controls, Lectro is confronted by a group of "skeleton" attack bots, which attack him on sight. After dispatching them easily, he questions why supposedly friendly bots would attack him. Godfather reassures him that they were merely rogues.
Lectro makes it to the turbine which produces the energy from the borehole, as he inspects it, he realizes nothing is wrong. That is when Sxullz and Grimm appear and attack Lectro. Confused, Lectro is no match and is quickly defeated. Being left for dead, Lectro is tossed into the sea, but not before he learns from Sxullz and Grimm's conversation that they were under orders from Godfather to get rid of Lectro...
Stage 1: Argendhal
Lectro is washed ashore and his circuits dry enough to allow him to move again. He attempts to regain his bearings, but since he cannot find any reference points, he concludes that he is very far away from the city. After looking for (and finding) a source of thermal emissions, Lectro finds the town of Argendhal, which is under attack by Godfather's bots. Lectro surmises that Godfather was not satisfied with Grimm and Sxullz's measures and has ordered his troops to ensure Lectro's total destruction.
Lectro finds that all his weapons have been lost and realizes the he must save the town so that he may be able to find replacement weapons. After he does so, the grateful townsfolk reveal to him that Godfather's bots have been seen elsewhere, and that without the energy provided by the city, human weapons are useless against them. The townsfolk also give Lectro his basic [plasma pistol] weapon, which had been found washed up on the coast.
Finally, Lectro learns that when the city was built, the 8 nations which contributed to construction were each given a keycode. When all 8 key codes are brought together, they de-activate the city's defence systems. Lectro now has an objective; find all 8 keycodes so he can shut down and repair the Godfather AI.
Stage 2: Vittorium
The first of these countries is the naval power of Vittorium. When Lectro enters, he is mistaken for a soldier of a hostile power, Carminium. Because of this, he is constantly attacked by Vittorian minion soldiers. Discovering that Vittorium's keycode is on display in a museum, Lectro fights his way into the museum, recovering his [autocannon] weapon (which had been found and mistakenly identified as an artifact) and the keycode.
Stage 3: Mapalyph
The country of Mapalyph has been completely overrun by Godfather's forces, who are actively looking for the keycode. Lectro has to recover his [EM sensors] from the riverbank at the end of the level before backtracking in a cutscene and using the sensors to find the keycode.
Stage 4: Armendal
The once proud country of Armendal is nothing but a blasted wasteland now. Lectro muses on the flaws in human nature before moving on to discover that Godfather's forces are combing the area to find the long-gone nation's keycode. Lectro has to use his EM sensors to find the keycode as well as his [flamethrower].
(I updated the 2nd post with this)