After sending out the signal to the other Arks, the player finds a quick-way back to the entrance (as with all bandit 'dungeons') and must return to Marshal. Subway town would be under martial law and you'd have to fight through the streets to get to Sual's garage. After which Marshal will tell you that everyone is packing up and relocating to another Town/(AKA quest-hub) and the resistance party takes the flying balloon to the next area.

As you fly in towards the next quest-hub you see there is a war raging across the wasteland below. Marshal comments about when he said "The War starts Now."
mission 1: Go save Ark survivors pouring into the wasteland.
mission 2: Liberate a bandit/authority weapons cache for them
mission 3: Gather other settlers who hate the Authority (Going back the Hager, Outrigger, Wellsprings, Survivors of Subway-town's martial law)
have an epic speech from Marshal
mission 4: Go assault General Cross's capital city
Where the assault through city streets fails, the resistance is crushed and you get captured

You come face to face with General Cross and he seems misunderstood. Saying the uneducated Wastelanders don't understand what he's doing. He explains to you that he was ordered to alter the timings of his and his men's Arks. This starts the next chapter of the game where the player is tasked to do a few minor jobs for the 'Authority' and will discover that other Ark Survivors live within the city and will discover that:

Apparently the president wanted the military to secure the Wasteland before any of the other Ark's opened to assess and neutralize any threats. What he found were hundreds of bandit tribes roaming the wastes and proceeded to destroy them one by one. While exterminating these bandit tribes, he accidentally wiped out a few settlements hence earning the 'Authority', as they began to call them, a bad reputation. A few years later while running experiments to increase the survivability of the average wastelander with nanotrites, by experimenting on captured bandits... Things went wrong- Creating mutants. Failures were discarded into the wasteland (as they were originally bandits). It wasn't until recently the mutants have multiplied and continued mutating, the Authority losing it's former Capital City (Dead City) as the threat became too great, and as a desperate measure General Cross authorized the creation of weaponized mutants.

Once the player is brought up to speed with these fetch-item-from-dangerous-place quests he is sent into the final stage of the game. Where you join an army of authority soldiers and mutants in a full scale war with an endless wave of mutants (either in the Wasteland or in another dead city) The final quest would be to go into the heart of the mutant nest (an underground and huge version those gory masses in Dead City) and to destroy whatever it is that's multiplying them. You head in with a small team- You battle waves of slime mutants- when you finally reach the final chamber you (or someone in the team) realizes that the mass itself is reproducing them and a PROPER I.D BOSS APPEARS AND YOU HAVE THE FINAL EPIC BOSS FIGHT RAGE DESERVED.

Then end credits.

Didn't read the whole thing, but i agree that there needs to be a end Boss. Finished the game yesterday after clicking those computers and throwing my advanced wingsticks at mutants. Was fun, but kinda easy. When you get in to that garage you get some sort of boss. Same for the Dead City, the big giant is pretty tricky when you don't shoot on time. But the end part is simply the most easy part in game. Just use the Pulse Cannon when things get out of hand, you own it like your in god mode. Hopefully a patch with some expansion stuff comes .

Also a sad thing is, that when you finished the last thing. The game returns to the main menu, so no grinding to 100 % if you have the feeling for that.

Good ideas. You don't propose an ending tho', rather a few more gameplay hours.

Yeah and you should perhaps take refuge in the town of Gun Barrel (mentioned earlier in the story)

As BigMutha says, heading to the town of gun barrel and having to deal with other bandit tribes also mentioned (Like the scorchers) would've been a good idea.

@Cimex actually the ending would've been that final boss fight- I feel it would've been a more satisfying climix than waves of authority mutants (:

This would actually be really awesome.

You should read the RAGE comics because your fantasy ending completely contradicts everything.