The ruling of Karrani dynasty ended when Daud Khan was defeated in the Battle of Rajmahal in 1576. Isa started playing a leading role in the local resistance. In the end he successfully conquered Dhaka, Rangpur, Pabna, Tripura, parts of Mymensingh and Bogra. In 1577, Isa established Egarasindhur (in present-day Pakundia Upazila,Kishoreganj) as the political and trading center. forming a petty kingdom that remained independent. He declared himself as the ruler of the Bhati region in 1581-82. From Sarail, he shifted his administrative centre to Sonargaon. He built fortresses at Katrabo, Kalagachhia and Khizrpur near Sonargaon.
Battle against Khan Jahan
In 1578 Mughal Subahdar of Bengal, Subahdar Khan Jahan led an expedition towards the Bhati region and set camp in Bhawal. Ibrahim Naral, Karimdad and Shah Bardi submitted their allegiance to the Mughal force. Isa faced the Mughal force led by Shah Bardi and Muhammad Quli on the Sarail-Juan Shahi border in Kastul on the bank ofMeghna river. According to Rajmala, Isa then quickly retreated to Tripura and sought assistance from the Tripura king, Amar Manikya. With the good grace of the queen Amrabati, the king granted an army of 52,000 to help Isa face the Mughals.
But before Isa returned to Sarail, two zamindars - Majlis Pratap and Majlis Dilawar already attacked and defeated the Mughal forces under Khan Jahan. Muhammad Quli was captured but Shah Bardi fled to Bhawal camp. With the remaining army, Khan Jahan retreated to Srihatpur city of Tandah. Few months later, Khan Jahan died of health issues on 19 December 1578.
According to descriptions by Rajmala, Khan, who became the Zamindar of Sarail, sent one thousand laborers for Amar Manikya along with other Zamindars of Bengal in response to the request made by Manikya to excavate the Amar Sagar Dighi at around 1580 AD. Besides, as the naval commander of Manikya, Khan fought against the Zamindar Taraf Fateh Khan in 1581 .
Battle against Shahbaz Khan
In 1583 Mughal General Shahbaz Khan destroyed Isa's palace in Baktiarpur. In September 1584, the then-subahdar Shahbaz crossed Ganges near Khizirpur and attacked Sonargaon, Katrabo and Egarasindhur. and pursued the defeated Pathan forces under Masum Kabuli up to Bikrampur in Dhaka, the cunning Isa then deluded negotiation of surrender and delayed the attack of Mughal general in several months. But in 1584 Isa and Masum Khan Kabuli deploying a muskets and gunpowder artilleries launched counterattack which finally defeat Shahbaz Khan in the naval and land battles of Egarasindur and Bhawal, and even killing one of Mughal general, then Shahbaz Khan retreated to Tandah.
Battle against Laksmana Singh Hajra
In 1585, he attacked two Koch rulers, Ram Hazra and Lakshman Hazra, and occupied their Jangalbari Fort (in present-day Karimganj Upazila, Kishoreganj ).
Another source from local tradition was recorded that this happened in 1586 after Man Singh had defeated him in the battle of Egarasindhur. In the same year, Mughal Subahdar Shahbaz Khan again sent his forces against Isa to the south.
Second battle against Shahbaz Khan
With the help of reinforcements by Emperor Akbar, Shahbaz Khan led another military expedition towards Bhati in 1586. Isa attacked him at Bhawal (north of Dhaka) but forces of Shahbaz Khan were well fortified near Brahmaputra. Isa then choose to give allegiance towards Akbar and prevented an imminent invasion of Bengal by the Mughals.
He even promised the Mughals he would dispatch Ma'sum Khan Kabuli, the renegade to a compulsory Pilgrimage to Mecca, something that viewed as an act of banishment. and although in the end he didn't do it, he did manage to restrain the rebel.
In late 1586 Ralph Fitch, an English traveler and merchant, came to Sonargaon, Bengal’s eastern districts and stated,
They be all hereabout Rebels against the King Zebaldin Echebar [ Jalaluddin Akbar ]: for here are so many Rivers and Ilands, that they flee from one to another, whereby his Horsemen cannot prevaile against them. The chief King of all these Countries is called Isacan [Isa Khan], and he is chief of all the other Kings, and is a great friend to all Christians.
Later on in 1588 he was involved in conflicts against Chand Rai and Kedar Rai
Battle against Raghudev
Isa continued his campaign against the Koch Kingdom. this time he fight and defeat Raghudev the king of Koch Hajo who ruled from Sankosh river in the west to the Bhareli riverin the east on the north bank of the Brahmaputra river and rival to Koch Bihar kingdom which gained prominence after the latter's annexation by Mughal empire. Isa successfully captured portions of Raghudev's territory as far as Rangamati and Goalpara. However, later Isa Khan and Raghudev formed an alliance against the threat of Mughal invasion
Battle against Durjan Singh
On 17 March 1594 Man Singh was appointed the Subahdar of Bengal by Emperor Akbar. After establishing Rajmahal as the capital of Bengal, Man Singh sent his own son, Durjan Singh, to Isa's Bhati region with a vast army on 7 December 1595. Isa was emboldened to resist the Mughals after he successfully sought alliance with Raghudev, his former enemy and Kedar Rai, Zamindar of Bhusna in Faridpur. In the clash that took in August 1597 and Isa engaged in a battle against Mughal naval forces with the assistance of Masum Khan Kabuli, an ex-Mughal defector. At first Isa faced defeat with the Mughals attacking Katrabo, one of Isa's pargana and city. However, on 5 September Durjan Singh was killed and Mughal was defeated. Both the army and navy of the Mughal-Koch Bihar alliance were either routed or captured.
It is recorded that in this clash Isa personally fought Man Sing in a duel. However the duel ended inconclusively when Isa Khan stopped fighting after Man Singh’s sword broke. The noble gesture touched Man Singh and both men was found respect for each other which developed into a friendship. Man Singh respect to his rival was even further that later when Isa sought to submit to the Mughal as the latter thought its wiser not to incite a full invasion, Man Singh accompany him to the Mughal court.
