She spent the next fifteen years with the newly renamed Terminus Foundation, eventually eradicating Lazar's disease for which she was awarded the
Universal Prize for Outstanding Achievement in Biochemistry. Initially intending to donate the entire sum of the prize money to the Foundation, she was persuaded by her then-lover and fellow Foundation member Travis — who was aware of her attemps to recreate the powers of the Keeper — to contribute a quarter of it to purchase the planet Sarabiss with him for the purposes of creating a new Traken Union. They and 50 other pioneers from the Foundation travel to Sarabiss only to discover that the supposed paradise has undergone severe and crippling ecological change within the space of a year. It is soon revealed that Travis had secretly accessed the plantary core of the planet in order to engineer it into a black hole which would become the power source for the Keepership, which he intended to usurp for himself as he believed he would be granted the power of a god.
During this time she was contacted by a time traveller named Tarkhal with a warning that at some unknown point in her past she had made a mistake that if corrected would result in the saving of many lives. Soon afterwards she was captured by forces working for a man named Myson, briefly added by the Gallifreyan mercenary named Fergurson, then confronted by Myson himself with the revelations that Travis had been his pawn, his plan was to turn the entire populance of Sarabiss into Keepers in order to gain the power of the Time Lords, and that Nyssa herself had been digitally encoded and recompiled with behavioural modifiers in place that prevented her from harming him. During this confrontation, Tarkhal secretly created a second, unaltered copy of Nyssa; both versions of her discovered that the Sarabissans were actually the decendants of the few people the original Keeper had managed to evacuate before the Union was destroyed by the Master's entropy wave.
The version of Nyssa in orbit subverted her conditioning long enough to crash the ship into an uninhabited landmass, killing herself and Myson. The unaltered version of Nyssa reset the Keeper device, freeing those who had been forcibly bound to the Source. Realising that her 'mistake' had been allowing too many people to take control of her life instead of exercising it herself, she kicked Tarkhal off the planet with the message that she missesd the Doctor, but not enough to want him back in her life. After punching out Travis — breaking his nose in the process — she arranged for his imprisonment in a deep hole somewhere a great distance away before agreeing to lead the remnants of her people in building a new Traken Union, but one without the need for a Keeper.