been a while since I posted in here, but I have 3 different ideas of how they could handle the story in SR4.
The first one is the retcon. I'm not the first person to mention this, but they could have SR3 be a movie created by Pierce. SR4 begins with The Boss' monologue from the Gangstas in Space ending. The End, credits roll, the camera pans out to show that we're in a movie theater, with Pierce and The Boss watching. Pierce looks to The Boss and asks how it was, Boss calls him a fucking idiot. The camera pans to Pierce's other side, where Gat agrees with him. Shaundi, complete with dreads and Eliza Dushku voice, peaks her head out from behind their seats (having just woken up from a weed-and-boredom-induced sleep) to ask if it's over with yet.
Cut to a shot of the logo, while the SR3 title screen music faintly plays in the background: The Next Great Sequel in the Saints Row Franchise.
That's probably the least likely of scenarios, though.
My second idea is to leave the shoes of The Boss entirely and start somewhat anew as a different member of the Saints. The game starts during the Three Way mission from SR3. You play as a random member of the Saints as you help fight against STAG and the Luchadors (this acts as the tutorial, naturally). Once the day is won, you're sent back to Stilwater, which you feel is an injustice, as you killed way more people than any other member besides The Boss himself (unfortunately for you, a lot of them were your own teammates)!
As a result, you and a motley crew of other disgruntled Saints members start planning a coup to take over the gang, which is immediately found out. You're kicked out of the gang (but not murdered, because after all, the Saints have gone soft). The first half of the game is spent building yourself back up in Stilwater so that, in the second half of the game, you can take the fight to the Saints in Steelport. The final battle is, naturally, against The Boss himself, first in a gunfight, then in a tank fight, then in a VTOL dogfight, and finally a QTE fist fight to the finish.
I thought of this idea because I truly feel like the story of The Boss has run its course, and part of what made SR2 so great story-wise was the way you worked your way up to the top. SR3 made you powerful right out of the gate.
The last idea, and most likely (as well as my most thought out), is just a straight sequel based off what SR3 established, combined with what little we knew about Enter the Dominatrix prior to its assimilation with SR4. It goes off of the Kill Killbane ending of Three Way, with Shaundi and Viola dead. Pierce is now officially second-in-command, Jenny Jaros is The Boss' understudy and de facto Shaundi replacement, Johnny Tag has been educated by Oleg to the point where he's practically the same as Gat, except really muscular and deep-voiced (which allows him to be VA'd without Daniel Dae Kim).
The game starts out with the same bank heist from SR3, but there are notable differences. Instead of Shaundi, it's Jenny in her alien costume, Tag instead of Gat, and Josh Burke is dressed up as Nyteblade. Instead of Morningstar, you're fighting mascots. After you blow up the vault, instead of an attack chopper, it's a giant disembodied Genki head.
At that point the screen statics and zooms out to reveal that it's a simulation that The Boss, who is strapped into The Dominatrix, is experiencing.
From there, the actual game begins. Once again, you have to start out at the bottom, since the aliens obviously won't give you anything. No more penthouse out of the gate, you have to live in an abandoned factory that you slowly transform into a pimp pad similar to the base in Stilwater.
More importantly, all 9 gangs from the Saints' past have been resurrected and are a part of one big super gang that controls virtual Steelport. Ultor is also antagonistic again, with Dane Vogel residing in the Phillips Building, which has been added to the downtown area. The first half of the game consists of re-experiencing previous missions with notable differences similar to the tutorial bank heist. Each time you kill one of the gang leaders again, you briefly hear Kinzie's voice calling out to you, but you think nothing of it.
Once you kill Vogel (who this time is driving a rocket mech from Red Faction Guerilla, which yes, will be pilotable in this game to go off of The Boss' desire to have one in the GiS DLC), the aliens surround the Phillips building. Despite all the absurd shit going on, aliens is where The Boss draws the line, finally realizing he's in a simulation. Kinzie gets in touch with him to reveal that she's logged into the Dominatrix manually, but now the aliens have found out and are trying to kill her, so Boss saves her and from there they try to find a way to awaken from the Dominatrix, which includes resurrecting (virtually) Gat, Carlos, and Aisha (going off of a comment in the April Fools post about how you'd see old friends again) and using the super powers.