It all began a few years before the Clone Wars, in the Old Republic, with the Outbound Flight.
A group of Jedi Masters and others decided to head out to another galaxy and see what was there. But before that particular expedition began, it was decided to send them and their ship on a shakedown cruise; a great circle cruise through part of the vast Unknown Regions.
A route, that was to bring it across the edge of territory controlled by the Chiss.
...The Outbound Flight never returned...
The Outbound Flight had already been decided by Palpatine to be a grave threat to his own ambitions, and he therefore send an assault force into the region to quietly take care of Outbound Flight when they showed up.
Palpatine's force were busily setting up their ambush when Thrawn found them.
On one side were handpicked units of Palpatine's own private army, equipped with fifteen top-line combat ships. On the other side were Commander Mitth'raw'nuruodo(Thrawn) of the Chiss Expansionary Defense and twelve small and insignificant border patrol ships.
After the battle, only a single one of Palpatine's ships remained capable of flight, and that only because Thrawn wanted some of the invaders left alive to interrogate.

Fortunately for that remnant, among the survivors was the leader of the task force, one of Palpatine's advisers. A man named Kinman Doriana.
Doriana explained the entire situation to Thrawn and convinced him that Outbound Flight had to be destroyed. Two weeks later, when the ship arrived in Chiss space, Thrawn was waiting. Goodbye, Outbound Flight.
Though that was the end of that, it was the beginning of trouble for Thrawn himself. The Chiss military philosophy did not recognize the morality of preemptive strikes. What Thrawn did was, in their minds, equivalent to murder.
Thrawn was, however, able to talk his way clear and retain his position, but from that point on the Chiss watched him very carefully.
Eventually as he dealt with some of the Chiss's enemies, he pushed things just a little too far. He was brought up on charges, stripped of all rank, and sent into exile on an uninhabited world at the edge of Imperial space.
...then Captain Voss Parck shoved up in his Victory Star Destroyer. He was willing to bring Thrawn back to Coruscant. There Captain Parck learned that Palpatine had made at least two unsuccessful attempts over the years to contact the Chiss and offer Thrawn a position with his soon-to-be Empire. Palpatine was most pleased with Parck's gift, though because of the political realities of the court he had to keep that pleasure hidden.
Thrawn went into private military training and eventually rose to the highest rank Palpatine could offer.
Once Thrawn was in position he returned to the Chiss territory, not to make the ruling Chiss families pay for they had done to him, but to protect them.
What was thought by the common Imperial, Thrawn and with him Parck had caused Palpatine's wrath and was send away from the galaxy with a single Star Destroyer on a mapping mission, it was all a part of a masterplan, it was all planned by the Emperor and Thrawn.

What did Thrawn achieve in the Unknown Regions?

It is not being told what Thrawn achieved in the Unknown Regions apart from claiming no less than 250 sectors! Mara concludes that the Empire probably has just a few actual colonies, but garrisons on all planets, listening posts, intelligence networks, full blown ship yards and a network of local allies. And that is just Mara's primitive conclusion!
This coulden't have been done with that single Star Destroyer Thrawn officially was given, no, the Emperor had been feeding Thrawn with ships, equipment and troops.
The Chiss is among the Empire's strongest allies and are supplying it with a steady stream of troops.

The threats in the Unknown Regions

Nothing is told by Admiral Parck except that "...there are a hundred different threats out there that would freeze your blood if you knew about them..."
The threats however are so horrifying, that on almost every planet in the galaxy, the Emperor and Thrawn have placed resistance cells, hardcore units ment to lead a rebellion to the threat, if and when it will conquer/destroy the galaxy.
Even Baron Soontir Fel, master Tie pilot, who once turned his back to the Empire and joined the Rebellion, has returned to the Empire, to join in the fight against the "unknown".
Baron Soontir Fel was origanally caught by Imperial Intelligence Director Ysanne Isard, and it is revealed that even she was under direct control by Thrawn, five years before his official reappearance.
Now he is fighting alongside Admiral Parck.

Kinman Doriana

Kinman Doriana was a "shadow adviser" - few people ever heard his name, let alone knew his postion and power. He had been Palpatine's right-hand man, supposedly one of the grand architects of his rise to power. Kinman Doriana's untimely death left a gap which Palpatine ultimately tried to fill with three other people: Darth Vader, Mara Jade and...Thrawn!

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