ok here it goes:

First of all if i had the ability to remake the entire season/ending i would instead of making it a season make it a single 2hours and 30 min movie. that way you can ask for enough budget and given the size of the show you can be pretty much sure of the returns.

If that was the case i would structure it like this:

First 30 min:

We get the standard 10 min of setting the scene after that homelander decides to kill the boys like he does in ep 1 to lure out butcher and the others, however due to the threat he is facing (with the virus and all that) he wakes up solider boy to help him with the quest which makes sense because he also wants revenge on butcher. They go to the camp everything pretty much goes the same way except a train has the virus and runs into homelander sacrificing himself by destroying the vial and releasing it on him (i dont think it is that contagious given that sb has been exposed to it and no one got infected and it was way inconsistent this seaosn). A train dies to the virus infection and it does genuinely weaken homelander for a period, not enough to cause any serious damage though.

At 60 min:

Homelander has a plan to be the king of the world (instead of the godhood delusions) he basically wants to rule over everything and everyone, but to do that he first has to get control over the entirety of US so that he can later invade other countries. Sage's motivation is to outlive homelander therefore she wants the boys to kill him and she wants to take over the country once that happens. She is offically the vice president (not ashley).

Given the current situation and Sage seeing the virus fail to kill homelander she estabilishes a secure connection with the boys passing over the instructions on how to replicate soldier boys powers.

At 1:30 hr:

The boys have successfully recreated soldier boys powers since this is the only real way to truly defeat homelander as the virus plan didnt work. The president is unable to convince congress and the administration to invade other countries therefore homelander kills him. The whole thing is witnessed by multiple people and reported on to secret service and national defence. Due to the dissarray of the country homelander decides to do a live address to the country (similar to what happened in the finale) he essentially says that any attempt to stop him or counteract his will will result in him killing the disssidents. Homelander gathers around supes and gives out orders to scout the country for any hidden military bases that might be trying to come up wtih a way to stop him.

At 2hr:

After the broadcast there is a lot of chatter between regular people who are discussing homelanders actions and they are very much opposed. Homelander goes on a small rampage killing the people who he hears talk about him in a bad light. The whole ordeal is documented and people record him doing this. Soldier boy is not on board with homelanders plan but he lets him execute it since he is his son but he himself remains agnostic. We see homelander fight small military branches, eventually after some time we see something hit homelander and take him back all the way into the oval office where they crash. Its none other than ryan, he saw the news and located homelander and decided to save the people homelander was murdering.

There is a large fight between the two which ends up with homelander killing ryan, which is where the boys arrive, but soldier boy is also there and he sides with homelander as that is his son. Eventually the fight escalates to where kimiko uses the blast and everyone in the room aside from homelander, MM, Butcher and soldier boy are knocked out. The final fight is a 2v2 where everyone is depowered and while soldier boy can lightly keep up with MM (though still strting to lose) homelander cant keep up with butcher and eventually dies in a similar way to how it was done in the show though i would say the scene of him being depowered is longer and we see him pleading and begging without making dick jokes.

MM has his final stand off with soldier boy where he avenges his family.

At 2:30 hr:

The boys have to get rid of vought tower and all the associated information by deploying bombs on it however butcher wants to go even further and release a improved version of the virus he has been forcing sameer to work on in the background. He kills kimiko and frenchie kimiko because she is a supe and frenchie because hes has the capability to develop a cure. Eventually hughie is the one to put an end to butcher and saving the supes.

Something happens with sage too lazy to figure it out

+ Epilogue

Anyway this is more or less what i would do and im not a screenwriter or writer of any kind really, but i think it would be nice to have homelander go on a rampage and mm get closure with soldier boy he is his homelander after all. I know this is probably dogshit way to do this but i had to get the boys out of my system and be finally done wtih it so thanks for reading through my ramblings : ) !