In 1583, he went through the posts of Chief of the Uigeumbu, Minister of Personnel, Rites and Military Affairs in a single year.

Also in 1589, Jeong Yeo Rip, a former Westerner who had switched factions to the more dominant Easterners, was accused of treason.

The Westerners took this opportunity to launch a purge and killed many prominent Easterners including, Jeon Yon Sin, Jeong Gae Chung, Yi Bal and more.

When it became time to appoint an heir to the king, Yi decided to take the opportunity to regain dominance for the Easterners and take revenge for the purge of 1589.

When the King asked the ministers who should become the Seja, Jeong Cheol and the Westerners recommended Prince Gwanghae while the Easterners Yi San Hae and Yu Sŏngnyong remained silent.

Meanwhile, the more conservative Easterners led by Yu Sŏngnyong were mostly students of Yi Hwang and suffered less during the purge so just wanted to settle for exile.

Yi San Hae was part of the Northerners and fearing that one day Jeong Chol would seek revenge, argued strongly for his execution.

After the fall of the Westerners, Yi had them all dismissed from court and replaced them by recalling the Easterners who had been removed during the purge.

Yi San Hae was the Chief State Councilor when the Japanese invaded in 1592, beginning the Imjin War.

Blamed for the initial military setbacks and the loss of the capital, Yi was exiled to Kangwon Province until 1595.

Yi San Hae was part of the Greater Northerners but largely stayed out of inter factional squabbles.

After Seonjo's death in 1608, Yi prevented a plot by the Smaller Northerners and ensured Prince Gwanghae succeeded to the throne.