Linyanti Swamp, Botswana (CNN) Scanning Botswana's remote Linyanti swamp from the low flying chopper, elephant ecologist Mike Chase can't hide the anxiety and dread as he sees what he has seen too many times before.

"I don't think anybody in the world has seen the number of dead elephants that I've seen over the last two years," he says.

From above, we spot an elephant lying on its side in the cracked river mud. From a distance it could be mistaken for a resting animal.

But the acrid stench of death hits us before we even land.

Up close, it is a horror.

Elephant ecologist Mike Chase examines an elephant whose face was hacked off by poachers in Botswana.

He was a magnificent bull right in his prime, 45 to 50 years old. To get at his prized ivory tusks, poachers hacked off his face.

Slaughtered for their ivory, the elephants are left to rot, their carcasses dotting the dry riverbed; in just two days, we counted the remains of more than 20 elephants in a small area.

Visitors and managers at the tourist camps here are frequently alarmed by the sound of gunshots nearby.

And Chase worries that if Botswana can't protect its elephants, there's little hope for the species as a whole.

AN UNPRECEDENTED SURVEY

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Chase, the founder of Elephants Without Borders (EWB), is the lead scientist of the Great Elephant Census , (GEC) an ambitious project to count all of Africa's savannah elephants -- from the air.

Before the GEC, total elephant numbers were largely guesswork. But over the past two years, 90 scientists and 286 crew have taken to the air above 18 African countries, flying the equivalent of the distance to the moon -- and a quarter of the way back -- in almost 10,000 hours.

Prior to European colonization, scientists believe that Africa may have held as many as 20 million elephants; by 1979 only 1.3 million remained -- and the census reveals that things have gotten far worse.

According to the GEC, released Thursday in the open-access journal PeerJ, Africa's savannah elephant population has been devastated, with just 352,271 animals in the countries surveyed -- far lower than previous estimates.

Three countries with significant elephant populations were not included in the study. Namibia did not release figures to the GEC, and surveys in South Sudan and the Central African Republic were postponed due to armed conflict.

In seven years between 2007 and 2014, numbers plummeted by at least 30%, or 144,000 elephants.

And the specific cases are even more disturbing:

In the Selous Game Reserve in Tanzania, and Mozambique's Niassa Reserve, elephant populations have plummeted by more than 75% in the past ten years as poachers cut down family herds, according to the survey.

The Babile Elephant Sanctuary in Ethiopia hasn't lived up to its name: Chase and the team counted just a single herd of 36 elephants -- the last in the Horn of Africa, a vast area roughly the size of Mexico.

A survey plane spots a herd of elephants in Botswana.

"When you think of how many elephants occurred in areas 10 or 20 years ago, it's incredibly disheartening," says Chase.

"Historically these ecosystems supported many thousands of elephants compared to the few hundreds or tens of elephants we counted."

The current rate of species decline is 8%, meaning that elephant numbers could halve to 160,000 in nine years if nothing changes, according to the survey -- and localized extinction is almost certain.

Even before the census offered proof, scientists calculated that far more elephants were dying than being born. Now the species has reached a tipping point.

AN EXTRAORDINARY INTELLIGENCE

Chase and other scientists feared they were in a race against time, which is where the Great Elephant Census came in.

The speed and scale of the project is unprecedented. Funded by Microsoft co-founder and Vulcan CEO Paul Allen, it brought together some of the best-known conservation groups and individuals, and teamed them up with the best bush pilots.

Small workhorse planes like the Cessna 206 were transformed into viewing platforms, using frames made up of rods -- in some cases telescopic golf ball retrievers -- fixed to the wing struts.

Observers on board the planes counted every elephant they saw within the grid, from Kenya's Maasai Mara to the Zambezi floodplains in Zambia.

As well as the GEC, Chase and his colleagues in EWB are tracking the movements of Africa's elephants using satellite collars which transmit real-time data on the elephants' movements.

Their work has brought to light signs of elephants' extraordinary intelligence, including evidence that they recognize a host of man-made threats -- and are willing to cross borders to escape them.

Northern Botswana is a well-known elephant corridor for herds moving from Botswana's arid Central Kalahari to the lush savannahs and forests of Angola and Zambia.

During Angola's long civil war, elephants avoided the country. After peace was declared, they moved back in -- but now, with the dramatic spike in ivory poaching, they're staying away again.

"This is really the front line," says Chase. "This is as far as they come. They will no longer move across eastern Namibia into Angola and Zambia, fearful of the consequences of poaching. Their home ranges have shrunk to within the relative safety and security of northern Botswana."

'WE'RE FAILING THE ELEPHANTS'

In northern Botswana, the Linyanti river's proximity to Namibia's Caprivi Strip -- a thin finger-like stretch of the country just 30 kilometers (18 miles) wide in parts -- makes it an ideal target for gangs of poachers.

"Poachers can act with impunity here, because there is nothing blocking their movements," explains Chase. "These borders are open to wildlife, and within a matter of minutes [they] can be in three different countries."

He looks through a neat record of GPS coordinates recorded in a leather bound notebook, listing possible elephant carcasses spotted by commercial pilots flying over the area.

Their corpses rot in the dry river grass down below. One bull's trunk has been hacked off and placed nearby -- the poachers' signature.

A bull elephant killed by poachers on the border of Botswana and Namibia, its face hacked off for its valuable ivory tusks.

The killers often don't even wait until the elephant is dead before they begin their ugly butchery.

The grotesque scene is repeated again and again across Africa's savannahs.

"I've been asked if I'm optimistic or pessimistic about the future of Africa's elephants, and on days like today, I feel that we are failing the elephants," says Chase.

AN UNCONVENTIONAL WAR

Botswana Defense Force troops patrol near the Linyanti.

Botswana is one of the last strongholds of savannah elephants. Along with South Africa and Zimbabwe, it accounts for more than 60% of all elephants tallied in the Great Elephant Census.

To protect the country's wildlife from poachers, the Botswana Defense Force (BDF) has deployed an infantry battalion of specially-trained soldiers; more than 700 are stationed across 40 bases in the far north.

In an immaculate camp on the banks of the Linyanti, a lieutenant lays out the morning's foot patrol on the detailed operations map.

The soldiers are armed with a controversial shoot-to-kill policy for poachers, but this is an unconventional war.

Despite their "shoot-to-kill" policy, troops are hampered by national borders they cannot cross.

"There is no clearly identified enemy," explains Brigadier Joseph Seelo. "The enemy can be everybody, an enemy could be someone we are living with on a daily basis."

Though poachers are often foreigners, Seelo says their deadly work is supported by locals, who help coordinate the teams, bury water and food, and mark the spots with GPS tags.

And every poaching team has at least one or two shooters; BDF officers say they're often ex-Zambian special forces, equipped with high caliber weapons.

A herd of elephants as seen from a survey plane flying overhead.

But many poachers across Africa are less sophisticated, emptying out the entire magazine of an AK-47 to pierce an elephant's tough hide, using poison-tipped spears, spiked traps and snares, or poisoning water holes.

In Angola, poachers even use grenades and mortars left over from the war to kill the animals.

"They will use anything that has the potential to inflict serious harm or kill an animal," says Chase. "This is a dismal fate."

"Who are we to sentence this animal to the verge of extinction using the most inhumane and cruel means?"

The remains of an elephant carcass on the border of Botswana and Namibia.

Despite the poachers' desire to make a quick buck, elephants are actually far more valuable alive than dead.

Every elephant killed will earn a poacher just a few hundred dollars -- the overwhelming majority of the tens of thousands of dollars its ivory fetches on the black market go to middlemen and organized crime gangs.

By contrast, a live elephant can earn more than a million dollars for communities involved in eco-tourism, according to a report from The David Sheldrick Wildlife Trust.

FACING INCALCULABLE ODDS

Veterinarian Larry Patterson prepares tranquilizer for an elephant collaring.

Larry Patterson carefully draws 14 milligrams of Thianil into a syringe, then inserts it into a long-range dart.

Even a tiny drop of the morphine derivative can kill a human, so the antidote is always close by.

Moments after being shot with the drug-tipped dart by the semi-retired veterinarian, a bull elephant snores loudly.

"These are emblematic creatures of the African continent, they are symbols of Africa, symbols of freedom," says Chase.

"These animals are facing incalculable odds. It's not just poaching, it's habitat loss, human elephant conflict, climate change. These are issues confronting us as well -- they're emblematic of the struggle for survival."

Promise the elephant comes to after being tranquilized.

"They are our living dinosaurs, the romance of a bygone era, and if we can't conserve the African elephants, I'm fearful to think about the fate of rest of Africa's wildlife."

Chase and Patterson thread a tracking collar around the animal's massive neck, fixing it with four bolts and a lead ballast.

We have to work quickly; the bull can't support his six-ton weight in the sedated position for long.

Before it wakes, Chase asks us to name the elephants.

We call him Promise, for the hope -- the promise, however faint -- that this creature's future can be secured.