The idea here is that Archer is forced to be as honest as possible from the very beginning of the war to the end, both about who he is and what he wants. I then want the holy grail war to have a completely different storyline from canon, in many major ways, while still retaining the base of the story. Finally, I want a group of all the allied forces in the war to end up going, or returning, to the Clocktower and wreaking havoc by existing as a group. This entire idea can be treated as on crack if you so wish to view it that way.
Since I still want this to be in line with his personality in canon,I want Rin to summon him as per usual, but then there's a difference. Once she sees how dishonest Archer is, I want her to use a command seal to make him honest the entire war, which basically makes everything devolve into chaos relatively quickly.
After Archer reveals who he is to Rin, she asks for details, of course. He explains that he's a counter guardian of Alaya, as well as how his life was for him in death. He also states that he wishes to cause a paradox by killing his past self, in hopes that it will free him from his eternal servitude. When he says he can't remember much about his life before death, Rin uses a command seal for him to remember all the details of what happened in his life while alive. (I'm not sure if this would actually work in canon, but I think that can be overlooked to some degree.) Archer then remembers how all three routes of canon Fate/stay night go, because he has experienced all of them before and just forgotten.
After having remembered specifically the route of UBW, Archer no longer wishes to kill Shirou. Instead, he hopes to just have a chat with Shirou about his ideals and make him realize what path they will lead him on, like he did with UBW's Shirou. He explains as such to Rin. First, however, she and Archer must figure out which route this Fate universe it set on. (Fate, UBW, or Heaven's Feel.)
they later find out that this universe is set on none of the three canon routes, but rather a new one entirely, and that's it's not just due to Archer's identity being known to Rin. Illya wants to meet her brother and have a chat with him, not kill him. Berserker is mostly sane, and Illya has access to the third true magic. Gilgamesh is interested in Shirou perhaps becoming a modern day hero, and does not care about his forgeries being an insult to him. Lancer is not under the control of Kirei, and Bazett (sorry if I butchered that name's spelling) is still alive and his master. Zouken's already been purified by Kirei, and Sakura freed of the worms. Rider was only summoned to help protect Shirou from the war. Kiritsugu is still alive and was never cursed, and he has also learned the fifth true magic by further studying his time alter ability. Shirou never made the mistake of turning his nerves into magic circuits. He also has higher tier magic circuits, and access to the first true magic to a degree that will only grow stronger as he learns more about it. It is common practice for servants to stay around after the holy grail war is over, and such practice has always taken place in prior wars as well.
So what enemy is left other than Angra Mainyu, once all the alliances are made between the groups? Well, Caster's still left unchanged, as is assassin, so they do need to deal with her and him. There's also Kirei to deal with, Saber still wants the grail to change the past, and Shirou will still become a counter guardian like Archer if left unchecked. Shirou should become similar to UBW Shirou, and he should fight with Archer like in UBW, just without Archer trying to kill him. Bazett likely also still wants the grail. Those are the things that need to be dealt with before we can move on to the Clocktower.
As for the people that are a part of the group of allied forces from the war, by the end of the war, which should happen relatively fast considering everything, we have Shirou, Saber, Rin, Archer, Illya, Berserker, Sakura, Rider, Kiritsugu, and Gilgamesh. Maybe if you want, you can have Bazett and Lancer ally with them too. So, basically, the group should be made up of the majority of the fifth holy grail war's combatants, with three that were around since the last war. (Saber, Kiritsugu, and Gilgamesh.)
Rin and Sakura go to the clocktower with their respective servants, (Archer and Rider) while Kiritsugu, Shirou, and Illya acquire high positions in the Clock Tower due to them having true magics, and they bring Saber and Berserker to help them out with their duties. Gilgamesh comes along too, opting to help out when he pleases. Lorelei and everyone else in the Clocktower tries to place restrictions on what the group can do, but to no avail. Everyone is baffled as to how three true magicians are in one group, and how all of the magicians, non-blood related or not, are related to each other.
If you want this to lead into a crossover, I'm not going to give you any ideas in that regard. I want to be surprised this time around, because I'm sure this can go somewhere interesting without me needing to interfere.