The storm rapidly weakened over land, but restrengthened in the Mozambique Channel to reach peak 10‑minute winds of 185 km/h (115 mph), making it an intense tropical cyclone.

The additional rainfall and flooding from Eline created the country's worst natural disaster in a century, and disrupted ongoing relief efforts.

A dam broke along the river, flooding the town of Chokwe in the middle of the night and trapping several unprepared residents; this accounted for nearly half of the death toll.

In the latter country, Eline dropped 503 mm (19.8 in) of rainfall in Levubu over three days, causing the Limpopo River to reach its highest level in 15 years.

The origins of Cyclone Leon–Eline were from a surge of energy within the monsoon trough that crossed the equator from the northwest, which spawned a low pressure area on 1 February in the eastern Indian Ocean, about 250 km (160 mi) south of the Indonesian island of Bali.

On the same day at 03:00 UTC, the Joint Typhoon Warning Center (JTWC)[nb 4] began issuing advisories on the storm as Tropical Cyclone 11S.

[3][4][5][6] Early on 5 February, the BoM upgraded Leon to a Category 3 severe tropical cyclone on the Australian scale, estimating 10‑minute winds of 120 km/h (75 mph).

[3] At 18:00 UTC that day, Leon crossed 90° E into the south-west Indian Ocean,[7] and as result was renamed Eline by the Mauritius Meteorological Service.

[7] Over the subsequent few days, wind shear caused the convection to wax and wane over Eline's center, limiting the thunderstorms to the southern periphery.

Moving back beneath an anticyclone, conditions became more favorable for strengthening, allowing outflow and a central dense overcast to form, with the beginnings of an eye feature.

Early on 16 February, Eline attained tropical cyclone status, with 10‑minute winds of 120 km/h (75 mph), while passing about 160 km (99 mi) northwest of Réunion.

[7] While in the central Mozambique Channel, Eline passed about 35 km (22 mi) north of Europa Island, which recorded a barometric pressure of 992 mbar (29.3 inHg).

[3] A brief increase in wind shear delayed the strengthening trend,[6] but Eline resumed intensifying on 21 February while slowly approaching southeastern Africa.

[7] While at peak intensity, Eline made landfall about 80 km (50 mi) south of Beira, Mozambique, where a central pressure of 989 mbar (29.2 inHg) was recorded.

Eline was unusual in maintaining its identity so far inland, aided by increased moisture and enhanced upper-level environmental conditions over southern Africa.

[8] Early in its duration while it was still in the Australian basin, the cyclone produced high waves near Christmas Island, forcing a boat of about 500 refugees to be escorted to port.

After Eline began restrengthening and turned more to the southwest, officials on Réunion declared a red alert, but this was dropped when the cyclone passed the island.

[10] When the storm moved ashore in eastern Madagascar, Eline produced strong winds along its path, with gusts estimated at 250 km/h (160 mph) by MFR at landfall.

[11] In Mahanoro, the biggest city near the cyclone's landfall in Madagascar, Eline disrupted power and water supplies while also leaving the town isolated.

[3] The floods were beginning to recede by the time Eline arrived,[23] and by the end of February 2000, the situation was considered the country's worst natural disaster in a century.

[25] By early March the floods were beginning to recede again, leaving behind a deep layer of mud,[26] ponds of contaminated water, and piles of rotten corpses.

[27] While Eline moved ashore, high winds knocked over coconut trees,[28] destroying over 250,000 ha (620,000 acres) of crop fields in conjunction with the floods.

[35] Also in Beira, the combination of strong winds and waves sank five ships in the harbor, including one at the entrance; this halted port traffic for about two weeks.

[3] Floods submerged the primary highway connecting the north and south of the country,[38] and damaged several other roads and rail lines, halting the region's economy by preventing movement of goods.

[29] In addition to the floods, strong winds blew away many roofs and some entire houses made of mud,[45] leaving thousands of people homeless.

In the latter country, Eline dropped 503 mm (19.8 in) of rainfall in Levubu over three days, causing the Limpopo River to reach its highest level in 15 years.

[10] The government of France sent two helicopters with teams of doctors to Madagascar,[57] and Médecins Sans Frontières sent about 35 tons of supplies, such as medicine, water purifying devices, and food.

[56][86] Many residents in flooded areas initially had to hold onto trees and roofs due to lack of helicopters,[87][88] with 100,000 people needing rescue as of March 1.

[89] After the floodwaters receded, the need for rescue diminished, allowing families to return home, although helicopters were still required to airlift relief goods.

[90] The United States sent a crew of 700 soldiers in what became Task Force Atlas Response, a $37 million operation to coordinate disaster relief, rebuild roads, deliver crop seed, and drop off aid.