An area of disturbed weather formed several hundred kilometers south-southeast of Okinawa on September 18.

Continuing to steadily intensify, Gene turned northwest and became a severe tropical storm on September 25.

Little development occurred over the next five days,[1] although the Japan Meteorological Agency (JMA) classified the disturbance as a tropical depression on the morning of September 22.

[2][nb 1] A Tropical Cyclone Formation Alert (TCFA) was issued at 06:00 UTC on September 23, followed by an increase in the disturbance's organization.

[4] Further development was aided by a tropical upper tropospheric trough to its west and the warm ocean waters of the Kuroshio Current.

Shower activity steadily increased and a Dvorak estimate of T2.0/55 km/h (35 mph) prompted the JTWC to designate it a tropical depression midday on September 23.

[1] Twelve hours later, the JMA reported that the depression had strengthened into a tropical storm,[5][nb 2] and after the system improved in organization and its outflow expanded,[1] the JTWC followed suit.

[4] Tropical Storm Gene intensified at the climatological rate of one T number per day as it tracked westward on a course initially resembling a straight runner.

Although restricted upper-level outflow prevented rapid intensification, a Dvorak intensity estimate of T4.0/120 km/h (75 mph)[1] lead to both agencies to declare Gene a typhoon on the evening of September 25.

[4] At 00:00 UTC on September 26, the JMA raised its intensity to 130 km/h (80 mph) for its maximum sustained winds, while the agency also estimated a minimum pressure of 965 mbar (28.5 inHg).

[2] However, the JTWC suggested that Gene was still slowly strengthening, and did not attain its maximum intensity of 90 mph (145 km/h) until 18:00 UTC that day.

[7] Gene recurved to the northeast on September 27 in response to a shortwave trough[1] while passing through the Ryukyu Islands.

[4] According to the JTWC, Gene maintained its peak intensity until 06:00 UTC on September 29,[1] although the JMA estimated that a weakening trend had begun six hours earlier.

[2] The typhoon continued to recurve and skirted Kyushu and Shikoku on September 29 before tracking just south of Honshu the following day.

[4] Based on surface observations, the JTWC downgraded Gene into a tropical storm at 06:00 UTC that day,[1] with the JMA doing the same at around the same time.

The JMA classified Gene as an extratropical cyclone at noon,[2] even though the JTWC did not follow suit until six hours later.

[14] Two people were killed in Miyazaki Prefecture because of landslides and another drowned into a river,[15] and an additional ten were wounded.

Throughout the prefecture, 4,688 houses suffered damage, while an additional ninety-two dwellings were destroyed, which led to 18,449 homeless.

[25] Seventy-five individuals lost their homes in Yamanashi Prefecture, where damage totaled to ¥716 million yen.