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Here's my (most likely inaccurate) predictions for the final 6 missions of Act 2:
S23 - Fatal Impact: The Soviet forces attempt to return to Earth using the Epsilon shuttles they recovered on the moon and attack Yuri directly in Moscow, however Yuri triggers the shuttles' self-destruct, causing most of them to explode on re-entry save, the one the General was on. The General must then go on the run and escape the Epsilon forces that swarm his shuttle's landing site, before rendezvousing with what's left of the main Soviet army to plan the attack on Moscow.
E23 - Reality Check: In the Epsilon HQ, Yuri informs the Proselyte that he's found a way to shield his forces from the Paradox Enigne's time freeze, the bad news is that the Allies are aware of it and have sent an advance force to destroy the Temporal-Psi arrays that are keeping the Epislon forces from being frozen in time. Yuri knows that this will be a stopgap measure but the goal is to drain enough of the Engine's energy by forcing it to keep chronoshifting more and more forces instead of engaging a single time freeze with which to wipe out the Epsilon forces, so that when the Allies launch their final assault the Engine won't have the power necessary to be of much use and will be easier to destroy. Basically it's a "hold the line until the timer expires" mission.
A23 - Withershins: A remake of the final Allied Mission in 2.0 "Scarlet Twilight", except with the Paradox Engine this time. Siegfried notes that the Engine is running low on power and as such the Commander can only activate the Time Freeze one last time. But first the Commander must destroy the Temporal-Psi towers that are keeping the Epsilon forces immune to the Time Freeze. Once the player does so, they are given the go-ahead to engage the time freeze and destroy the Mental Omega Device. However in a dramatic twist on what was up until this point a running gag, Siegfried has miscalculated, the time freeze collapses and the machinery that generates it burns out, before the player's forces can reach the Mental Omega Device and the Paradox Engine finds itself right in the middle of Epsilon's forces. Given a choice between either destruction or escape via Chronoshift, Siegfried engages the Paradox Engine's Chronosphere, channeling all of the Engine's remaining power into it to make one final Chronishift, saving the Commander and the Engine, which promptly begins to fall from the sky over the Bearing Strait.
S24 - Death's Hand: The General leads the attack on Moscow, in a remake of "Red Revolution" from RA2, firstly by sending in Krukov, Reznov, Volkov and Chtzkoi to sneak into the Kremlin grounds and destroy the Psychic Beacon keeping Moscow and it's contingent of Russian troops mind controlled, afterwards, the player much track down Yuri who is attempting to flee to an Airport north of the Kremlin (in a role-reversal remake of "No Dilemma" from 2.0), and destroy all the Epsilon forces in Moscow. But as it turns out, it was a trap set by Yuri, who activates a second Psychic Beacon hidden in the very Kremlin, mind controlling the entire Russian force, who proceed to kill the heroes, and further deploying the titular "Death's Hand" super-MIDAS rocket, loaded with conventional explosives against his HQ in Antarctica.
E24 - Babel: With the Paradox Engine gone, the remaining Allied forces in the Antarctic, led by Norio and Tanya, decide to go for broke and destroy the Mental Omega Device, the Proselyte must hold off the initial attack wave and then launch a counter attack that will destroy their last base in the Antarctic, killing Norio and Tanya in the process. Yuri then contacts the Proselyte and instructs him to send Libra into the Mental Omega device. Once that is done the Death's Hand impacts and destroys the device, unleashing a psychic shockwave that, while harmless to psychics, saps the willpower of any normal human making them even easier to mind control, he then reveals to the Proselyte his true plan, to use the Psychic Amplifiers he has already constructed to mind control most of the planet by increasing their range to maximum, relying on mankind's compromised willpower from the shockwave to keep them under his control despite the Amplifiers' lowered power output in order to maintain their range of effect. He points out that there is one final loose end, and that is the downed Paradox Engine.
A24 - Hamartia: The remaining Allied forces flee the semi-floating but damaged beyond repair Paradox Engine to the nearby shores of Alaska. They've already received reports that Yuri's plan has succeed and most of the world is under his control now. He's won. And he has sent forces their way to mop up their remaining forces and ensure that the Paradox Engine is destroyed. The mission revolves around navigating through the Alaskan coastal wilderness and finding a safe place for Siegfried and Yourself (the Commander as an in-game mission unit) to plan their next moves. They are then contacted by Yunru's proto-Foehn force, and provide the surviving Allied forces with rendezvous co-ordinates. Once the co-ordinates are reached, the Commander and Siegfried meet up with Yunru, who explains exactly what's happened to the world and now that the Allies and Soviets are gone, they must work together to create a Revolt that will topple Yuri's dominion.
Why do I feel this is basically what happens in the final few missions?
Though admittedly nicely elaborate and interesting, I find a few parts to be doubtful.
For Soviets, the recent Covert missions like Brothers in Arms and Dawnbreaker feature their forces gathering in geographic locations far off from each other. I cannot claim to have a good idea about the exact sequence of how the last two Soviet missions go, but the missions and the narrative have built to at least one epic slugfest between them, with the forces from said locations joining you as reinforcements.
As for Allies, I have mentioned in before, but I can't see anything that would suggest that SIegfried is going to live through Act II.
