Said changeling secretly formed The Alliance: an alliance between the True Way, Breen, Tholians, and T'Ket, with the objective of defeating the Infamous Armada, a top secret organization, pretty well criminal in some ways, that had been pulling strings on various leaderships and doing other things we don't hear about.
The Undine attack Earth Spacedock, and the station is equipped with devices that can repel Undine, and Borg (only if they're connected to the/a Collective outside the station; mini collectives can operate inside the station exclusively without any difficulty).
Some of the prisoners die by the hands of Omega Operatives, others are recaptured after an escape. They find out about The Alliance.
Sarah, captaining the prime universe's USS Sally, pursues. The Sally ends up being destroyed by the Firestorm, but the Firestorm is retaken while the changeling admiral and the admiral's senior staff (who don't know he's a changeling and have been lead to believe The Alliance isn't what it seems) escape to a Cardassianstarbase, steal a ship, destroy a Starfleet escort, and then run.
Angry about The Alliance briefly stealing the Philadelphia to examine it for anti-Iconian devices, the Infamous sends his Q minion to make the changeling Admiral Nat suffer. Said changeling then calls on Q-Junior, who, for unknown reasons, grants the changeling access to the heart of the storm, the center of the universe and means of unlocking ridiculous power. Changeling Nat becomes a super-Q and seals off the Q continuum entirely, at least for a while.
11 of 14 eventually learns the truth and defects back to Starfleet, eventually joins Sarah's crew aboard a new ship, some Nova class science vessel, the USS Molly, which is sent out to explore the Natara Expanse.
They discover a wormhole to another universe, where Nat and Sarah's roles are swapped. By request from their Captain Nat (the same one we know now), the wormhole is destroyed, stranding Captain Nat and his small crew, and ship, in our universe.
The same universe's changeling Sarah had already unlocked super-Q powers, came to our universe and allied with our changeling Nat.
Our USS Molly crashes, Sarah is kidnapped by the Infamous Armada's flagship, and the alternate USS Molly (having rescued the prime version's crew) narrowly escapes after being nearly destroyed by the CBS Falzon, a Breen Rezreth-classDreadnought captained by ThotTran, who had been previously posing as a defector and ally of Starfleet. Captain Terry was also present aiding the Falzon until they discovered the Breen ship was actually there to destroy the Nova-class ship, rather than rescue it like they recruited the USS Kitana for.
The 2 galactic Hyper Powers nearly go to war that would have certainly wiped out the entire galaxy, but The Alliance eventually retreated to the Andromeda Galaxy aboard the Natara, Sarahara (alternate universe's equivalent of Natara), and Andromeda Dyson Spheres.
Sarah Walker is freed, barely having kept her marbles through the horrible experience that probably still spawns nightmares.
The Firestorm's Q power draining capability is revealed, draining changeling super-Q Sarah of her power and transferring it to now Hyper-Q changeling Nat.
Sarah briefly helps command a Starbase alongside Captain Nat, but is captured again after changeling Sarah (who had been overthrown by changeling Nat and then given a hyper-godship by her future self) attacks the Starbase. The Infamous is "killed" when trying to form an Alliance with the alternate changeling Sarah Walker, only to be captured by changeling Nat. The Infamous's consciousness leaves that body, leaving it as just another clone.
Another Infamous ends up declaring Krystal the next Infamous Armada leader, although fails to actually give out the necessary command codes for that to work. There's also some kind of ceremony for mourning recent deaths, which none of my own characters were involved in (although changeling Nat certainly watched from a viewscreen somewhere).
Captain Nat, Changeling Sarah, and Krystal Jade get kidnapped by Regent Nat to help him get rid of Leeta.
Changeling Sarah is revealed as a changeling and promptly captured, and the real Admiral Nat is later rescued, his crew are freed, but probably now on a watchlist...
The changeling Nat's captured Infamous (now clone) ends up being forced into his bidding and is called on, left behind and ends up giving Krystal the codes to take command of the armada. She did so, which I believe caused a signal awakening the final Infamous... who also ordered all the other Infamous clones killed.
The armada largely vanishes into the shadows. Another Infamous, the final one, awakens and attacks a Prometheus-class ship and turning it's crew to loyalty for the Infamous, only for the admiral to attack with a battlefleet, effectively rescuing the Starfleet vessel and forcing the Infamous forces to retreat (they have since never returned).
Changeling Nat's powers are drained, and Captain Nat ends up agreeing to take on the powers for himself, hoping to keep them out of the way so they don't become a problem.
Krystal makes peace with The Alliance, who free the Dominion from Infamous Armada control entirely.