In 1583, he escaped from the prison and with the help of the nobles succeeded to regain the throne for a short period before being defeated by Akbar's general Abdul Rahim Khan-I-Khana in January 1584.
The nobles unwilling to crush the Fauládis, fearing lest their turn might come next, entered into secret correspondence with them, and withdrew when battle was joined.
Sayad Mírán also left Áhmedábád for his estate at Dholka, and joining Tátár Khán at Ranpur they both went over to the Fauládis at Pátan.
He was met by the Fauládis near the village of Jotana, about thirty miles south of Pátan, where he was defeated and compelled to return to Áhmedábád.
At this time the Mírzás, who were the sons of Sultán Hussain of Khurásán, quarrelling with Jalál-ul-dín Muhammad Akbar, entered Gujarát, and joined Changíz Khán.
The Habshis now plundered Changíz Khán’s house, while the Mírzás, mounting, went south and took possession of Bharuch, Baroda (now Vadodara), and Champaner.
Sultán Muzaffar Shah III, who had separated from the Fauládis, fell into the hands of the emperor, who granted him his life but placed him under charge of one of his nobles named Karam Áli.
The emperor recalled the detachment he had sent against Surat, and overtaking the Mírza at Sarnál or Thásra on the right bank of the Mahi River about twenty-three miles north-east of Nadiad, after a bloody conflict routed him.
The emperor now sent a force under Sháh Kuli Khán to invest the fort of Surat, and following in person pitched his camp at Gopi Talav, a suburb of that city.
After an obstinate defence of one month and seventeen days, the garrison under Hamzabán, a slave of Humáyún’s who had joined the Mírzás, surrendered.
Under his invitation a large party of Portuguese came to Surat during the siege, but seeing the strength of the imperial army, represented themselves as ambassadors and besought the honour of an interview.
Sher Khán again took refuge in Sorath, and his son fled for safety to the Ídar hills, while the Mírza withdrew to the Khándesh frontier.
Muzaffar remained for some time in the Rajpipla, and thence came to one Lúna or Lúmbha Káthi, at the village of Khíri in the district of Sardhár in Sorath.
At this time a party of 700 or 800 Mughals, called Wazír Khánis, separating from Shaháb-ud-dín, remained behind in hope of being entertained by the new viceroy.
As Ítimád Khán declared that he was unable to take them into his service, they went off in a body and joined Muzaffar at Khíri, and he with them and three or four thousand Káthi horse marched at once on Áhmedábád.
The fort of Bharuch was also at this time traitorously surrendered to Muzaffar by the slaves of the mother of Naurang Khán, fief-holder of the district.
Muzaffar, who was still at Broach, hearing of the advance of the new viceroy with a large army, returned rapidly to Áhmedábád, and in 1584 fought a pitched battle with Mírza Abdúr-Rahím Khán between Sarkhej and Sháh Bhíkan’s tomb.
Bharuch now submitted, and Muzaffar sought shelter with Amín Khán Ghori at Junagadh, by whom he was allotted the town of Gondal as a residence.
He advanced to Morbi, and thence made a raid on Radhanpur and plundered that town, but was soon compelled to return to Kathiawad and seek safety in flight.
Amín Khán, seeing that his cause was hopeless, on pretence of aiding him, induced Muzaffar to give him some money, two lakh Mahmudi.
The Jám of Navánagar and Amín Khán sent their envoys to meet the viceroy, declaring that they had not sheltered Muzaffar, and that he was leading an outlaw's life, entirely unaided by them.
When he reached Upleta, about fifteen miles north-west of the fortress of Junágaḍh, the viceroy heard that Muzaffar had sought shelter in the Barda hills in the south-west corner of the peninsula.
Advancing as far as Morbi, Naurang Khán entered into negotiations with the Jám, who, however, refused to accede to the demands of the imperial commander.
Still the fortress held out, and though the viceroy joined them the siege made little progress as the imperial troops were in great straits for grain.
Without halting Naurang Khán started in pursuit, nearly surprising Muzaffar, who escaping on horseback with a few followers, crossed to Cutch (now Kachchh).
Sewa Wádhel covering Muzaffar’s retreat was surprised before he could put to sea and fought gallantly with the imperial forces till he was slain.
Naurang Khán then came to Arámra, a village belonging to Singrám Wádhel, Rája of Dwarka, and after frustrating a scheme devised by that chief to entrap a body of the troops on board ship under pretence of pursuing Muzaffar’s family, led his men back to Junágaḍh.
At the same time the Cutch chief, who is called Rao Bháramalji I, sent a message that if the viceroy would refrain from invading his country and would give him his ancestral district of Morbi and supply him with a detachment of troops, he would point out where Muzaffar was concealed.
[2] The detachment, strictly guarding the prisoner, were marching rapidly towards Morbi, when, on reaching Dhrol, about thirty miles east of Nawanagar (now Jamnagar), under pretence of obeying a call of nature, Muzaffar withdrew and cut his throat with a knife, so that he died.