Kepler arrived at the Benatek observatory on February 4, 1600, and Tycho was pleased to see him – for Tycho needed Kepler as much as Kepler needed Tycho. Kepler had come to Tycho hoping that Tycho would share his observations of the stars and planets, as Kepler needed the data to perfect his universe of perfect solids. But Tycho was secretly hoping that Kepler would reconsider this plan. Tycho had his own theory of how the universe was constructed. He imagined that the sun revolved around the earth and the other planets revolved around the sun. Tycho hoped that Kepler would help him develop the system so Tycho could take his place among the great names in astronomy.

If Kepler had been hoping for a new mentor, he must have been sorely disappointed. Tycho treated Kepler like a family dog, and not a particularly well-loved one. Tycho refused to pay Kepler the salary he had been promised, refused to share any more observations with him than were absolutely necessary, and forced Kepler to waste his time writing attacks on Tycho's enemies. Their short relationship was filled with bitterness and fighting. Several times Kepler left the lab in anger, only to return days or weeks later begging Tycho's forgiveness.

Kepler was trapped. In July of 1600, he was permanently expelled from Gratz, along with the rest of the town's Protestants. Kepler once again turned to Maestlin for help and, once again, Maestlin declined. He did not respond to Kepler's letters for another five years. It was a miserable moment for Kepler, but a fortunate one for Tycho, as it meant that Kepler had nowhere else to turn.

Frustrated as he was about his relationship with Tycho, once Kepler went to work in the lab, nothing could have distracted him from the problem at hand. As the most junior member of the staff, Kepler had been assigned to work on the orbit of Mars: the trickiest and thus least desirable of the planetary orbits. Kepler was undaunted, and even bet one of his colleagues that the task would take him only a week. It eventually took him seven years – it would be the most frustrating and most fruitful years of his life.

Kepler and Tycho's relationship was short-lived. On October 13, 1601, Tycho went to a fancy dinner with the Baron Rosenberg and a number of other members of upper crust society. As Kepler recorded, Tycho was too polite to leave the table to use the bathroom, instead putting an unhealthy amount of pressure on his bladder. According to Kepler, this caused the infection that killed him less than two weeks later.

Tycho's last words seemed directed at Kepler: "Let me not seem to have lived in vain," he pleaded. But Tycho's pleas fell on deaf ears; Kepler would not raise the Tychonic planetary system to the glory that Tycho had hoped. Instead, Kepler finally got a hold of Tycho's observations and used them to create a new vision of the Copernican universe.

After Tycho's death, Kepler was appointed to his position as Rudolph II's Imperial Mathematicus. This title carried prestige and a salary, meaning that Kepler could finally afford to immerse himself in his studies. He worked on the orbit of Mars for five more years and then, when he was finally ready to publish, was almost prevented from doing so by a petty family feud.

Kepler had based all his research on Tycho's observations – the same observations that Tycho had so jealously guarded during his lifetime. After Tycho's death, Kepler took advantage of his access to the lab. Without asking anyone's permission, took the observations for himself, reasoning that he was the only one who could make good use of them. When Tycho's family realized this, they went on the offensive. Led by the Junker Tengnagel, Tycho's son-in-law and former assistant, the Brahe family tried every legal strategy they could think of to gain control of the observational data. As the Brahes had powerful connections at court, Kepler was left at their mercy. The feud took four years to resolve, until, in 1608, Tengnagel finally gave permission for the book to be published. The Astronomia Nova was finally published in 1609; it would be Kepler's most important work.