Here's how things would've gone.
The strange organization was a cult that followed Bill Cipher. After his defeat, they prepared for Dipper and Mabel's return. They needed all members of the Zodiac so that they could conduct a ritual to resurrect Bill. The Zodiac was intended to be a double sword of sorts that could either banish Bill, or bring him back if used in the wrong way.
The cult needed the magic essence of the whole Zodiac in order to bring Bill back. Knowing they would never do this willingly, the cult sacrificed people and used their bodies to bring back past, evil incarnations of the Zodiac, under their control. They would steal the essence of the current incarnations, preferably kill them, and perform the ritual.
The golems would have special powers. Examples being...
Stitched Heart: Strength and Hallucinations
Glasses: Machinery
Shooting Star: Small Meteors
Pentagram: Telekinesis
Where we left off, Sixer and Shooting Star attacked at the same time. Sixer would not walk away, but Shooting Star would escape. After this, the Pines would put two and two together and begin warning the other members of the zodiac.
Gideon, Pacifica, and Robbie would join the Pines in defeating the resurrected Zodiac. They would've gotten character development. Gideon and Robbie striking up a friendship, Gideon starting to move past Mabel, Robbie and Dipper coming to some sort of understanding, Pacifica and Mabel finding some stuff in common, mayyyybe some dipcifica hints.
Meanwhile, the voice in Dipper's head would be revealed to be the past Pine Tree, whose powers influenced minds. He'd continue trying to break Dipper, slowly taking control throughout the story. This would strain Dipper's relationship with Mabel.
Despite being able to beat most of the Zodiac, a powerful counterattack by the cult of Bill would trap the team and take them hostage. The current Zodiac team would eventually escape and hurry to stop the ritual, eventually finding and capturing the cult leader, gaining an advantage. It would be here that the cult leader, at the height of Dipper and Mabel's strain, would reveal that Mabel gave Bill the rift, starting Weirdmaggedon.
By this time, Dipper's mind would be pushed to the brink, and the shock would be enough for Pine Tree to fully take over. The Pines would stay behind to stop him as the rest of the team hurried to stop the ritual. Mabel would have to confront her flaws and negative treatment of her brother, and take responsibility for inadvertently starting Weirdmageddon (assuming she remembered giving Bill the rift and simply decided not to say anything). The Pines family would eventually be able to snap Dipper out of it, Dipper's will empowering Pine Tree's and expelling him from his mind forever.
Bill would be resurrected for all but a minute, but due to the ritual being halted by the Pines and their allies (and a sacrifice from McGucket, yes, he was intended to die stopping the ritual), his form would be too unstable, causing an explosion which would destroy the cult base.
The team would make it out. A week at the hospital and a funeral for McGucket. Things would slowly go back to normal. The epilogue sees Dipper and Mabel's siblingship back to how it was before Pine Tree's influence, but a little better (getting some development they unfortunately didn't get in Weirdmaggedon). Things start looking up again. The End.