The cyclone steadily weakened due to persistent land interaction and dry air, remaining quasi-stationary for two days before slowly drifting offshore as a much weaker system; the storm dissipated on 4 November over the Bay of Bengal.

Although its primary effects were felt in a localized area of India, the outer fringes of the super cyclone impacted Myanmar and Bangladesh.

The 5–6 m (16–20 ft) surge brought water up to 35 km (20 mi) inland, carrying along with it coastal debris and inundating towns and villages.

Alongside foreign and domestic government contributions, between 12 and 14 international aid agencies concurrently participated in relief efforts in the storm's aftermath.

Tracking westward, the disturbance encountered a more favorable environment in the South China Sea; as a result, thunderstorm activity began to increase.

Prompted by these changes, the Joint Typhoon Warning Center (JTWC) issued a Tropical Cyclone Formation Alert (TCFA) at 02:00 UTC on 23 October.

However, the system failed to develop any further before wind shear reemerged in the Gulf of Thailand, causing convection to diminish and resulting in the cancellation of the TCFA.

Although the environment remained moderately unfavorable for tropical cyclogenesis, the disturbance organized, developing fair outflow, a strong rainband, and additional convection.

[9] Using the Dvorak technique, the IMD estimated that BOB 06 reached its peak intensity three hours later with maximum sustained winds of 260 km/h (160 mph) and a minimum barometric pressure of 912 mbar (hPa; 26.93 inHg);[1] this made BOB 06 the strongest tropical cyclone ever recorded in the North Indian Ocean by pressure with sustained winds at the time matched by only two other known cyclones in the Bay of Bengal.

[1] Although the storm's organization and appearance deteriorated as it neared land, BOB 06's intensity held steady up until it made landfall on the Odisha coast between Puri and Kendrapara at 06:00 UTC on 29 October.

[1][2] Rather than moving inland as forecast, the tropical cyclone became quasi-stationary over the coastal Jajpur area as it laid within a weak steering region between two upper-level anticyclones.

[2] Soon, the weakening storm became caught in a mid-tropospheric wind flow, inducing a southward drift that brought BOB 06 back over the Bay of Bengal.

The cyclone continued to weaken over water, and the IMD stopped monitoring the storm on 31 October;[1] the JTWC followed suit a day later.

Due to initial uncertainty in the storm's forecast track, the first warnings for the coast of mainland India on 27 October concerned northern Andhra Pradesh, Odisha, and West Bengal.

[6] The Indian Department of Agriculture and Cooperation (DAC) served as the primary administrative body for coordinating preparatory and relief work during the 1999 Odisha cyclone.

Six districts maintained 23 permanent cyclone shelters operated by the Indian Red Cross Society, eventually serving to house 30,000 evacuees.

[13] Passing south of Bangladesh, the 1999 Odisha super cyclone's northern fringes swept across the country, killing two people and initially causing 200 fishermen to go missing.

[6] Twelve districts of Odisha suffered severe damage, reporting complete breakdown of essential services: Balasore, Bhadrak, Cuttack, Dhenkanal, Jagatsinghpur, Jajpur, Keonjhar, Kendrapara, Khurda, Puri, Mayurbhanj, and Nayagarh.

[18] Along the Odisha coast, the cyclone generated a 5–6 m (16–20 ft) storm surge that brought water up to 35 km (20 mi) inland, inundating a large swath of coastal areas.

The inundation induced by the far-reaching storm surge and heavy rain kept Konark submerged in knee-deep water for six days after landfall.

[2] Oswal Chemicals and Fertilisers, which maintained the world's largest diammonium phosphate plant, reported severe damage to the facility.

[16] Damage sustained to various sanitation infrastructure led to a heightened risk of communicable disease outbreaks; indeed, diarrhea and cholera saw increased incidences following the storm's impact.

The area's vulnerability to disease was also compounded by a lack of pre-storm vaccinations, raising fears of a potential measles outbreak.

[34] The Central government also considered the establishment of a Department for Natural Disaster Management to handle the devastation caused by the cyclone.

[35] The Indian Army sent infantry, engineers, and signal detachments to assist with disaster relief, including a field medical unit containing 30 ambulances and 340 doctors.

[33] Indian Air Force helicopters dropped food packets in affected regions beginning on 30 October, while other government ground personnel distributed various relief supplies including vaccines and plastic sheeting.

[13] Due to severe damage to air traffic control infrastructure, the Biju Patnaik International Airport was closed until 2 November, curtailing relief operations.

[22] In response to the storm's devastation, Oxfam prepared an initial aid package,[39] including emergency water equipment worth £250,000 (US$306,665) and 50,000 instant meals.

[13] CARE carried over its preexisting relief operations from the early October cyclone, routing food supplies by train to hard-hit locations in Odisha.

[31][45] Runoff caused by the cyclone enhanced available nutrients in the Bay of Bengal, supplementing the already present equatorward ocean current and resulting in an increase in chlorophyll a and particulate organic carbon in the region.