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Spy wars: How the CIA set up its secret bases in Ukraine

For more than a decade, the US has developed a covert intelligence partnership with Ukraine that is now crucial for both countries in confronting Russia, The New York Times reports.

Nestled in a dense forest, the Ukrainian military base appears abandoned and ruined, its command centre a burned-out hulk damaged by Russian missile fire at the start of the war. However, that’s what’s above ground.

Nearby, an inconspicuous passageway leads to an underground bunker where groups of Ukrainian soldiers monitor Russian spy satellites and eavesdrop on the conversations of Russian commanders. On one screen, a red line traces the route of an explosives-laden drone as it makes its way through Russian air defences from a point in central Ukraine to a target in the Russian city of Rostov.

The underground bunker, built to replace a destroyed command centre in the months after the conflict in Ukraine began in February 2022, is the secret nerve centre of Ukraine’s armed forces. The base is almost entirely funded and partly equipped by the CIA. General Serhiy Dvoretsky, the intelligence commander, said in an interview at the base:

One hundred and ten percent.

Now in the third year of a bloody conflict, Washington and Kyiv’s intelligence partnership is the linchpin of Ukraine’s ability to defend itself. The CIA and other US intelligence agencies provide intelligence for targeted missile strikes, track Russian troop movements and help maintain spy networks, according to The New York Times.

But this partnership was not created in wartime, and Ukraine is not its only beneficiary.

It was born a decade ago, emerging piecemeal under three different US presidents, and promoted by key individuals who often took bold risks. As a result, Ukraine, whose intelligence services were long considered thoroughly compromised by Russia, has emerged as one of Washington’s most important partners in the fight against the Kremlin.

The listening post in the Ukrainian forest is part of a CIA-backed network of spy bases established over the past eight years that includes 12 secret sites along the Russian border.

Around 2016, the CIA began training an elite Ukrainian commando unit known as Unit 2245, which captured Russian drones and communications equipment so that CIA technicians could repurpose them and crack Moscow’s encryption systems. (One of the officers in this unit was Kyrylo Budanov, now the general in charge of Ukraine’s military intelligence.)

Moreover, the CIA helped train a new generation of Ukrainian spies who operated inside Russia, in Europe, Cuba and other places where the Russians have a large presence, The New York Times reports.

The relationship was so entrenched that CIA officers remained in a remote location in western Ukraine when the Biden administration evacuated US personnel weeks before the outbreak of military conflict in February 2022. The officers relayed crucial intelligence during the outbreak of hostilities, including where Russia planned to strike and what weapons systems it would use. Ivan Bakanov, who at the time headed Ukraine’s domestic intelligence agency, the SBU, said:

Without them, there would have been no way for us to resist the Russians, or to beat them.

The details of that intelligence partnership, many of which The New York Times is revealing for the first time, have been a closely guarded secret for a decade.

In more than 200 interviews, current and former officials from Ukraine, the US and Europe described a partnership that nearly fizzled out over mutual distrust but then steadily expanded, turning Ukraine into an intelligence-gathering centre that intercepted more Russian communications than the CIA’s Kyiv office could initially process. Many of these officials spoke on condition of anonymity to avoid discussing intelligence and sensitive diplomatic matters.

Those intelligence networks are more important now than ever, as Ukraine increasingly depends on sabotage and long-range missile strikes that require spies far behind the front lines. And they are increasingly at risk: If Republicans in Congress cut off military funding for Kyiv, the CIA may have to scale back its operations.

To try to reassure Ukrainian leaders, William J. Burns, director of the CIA, made a secret visit to Ukraine last Thursday – his 10th since the military conflict began, according to The New York Times.

From the beginning, the CIA and its Ukrainian partners have been united by a common adversary – Russian President Vladimir Putin.  According to a senior European official, in late 2021, Putin was considering whether to launch a full-scale invasion when he met with the head of one of Russia’s main spy services, who told him that the CIA, along with Britain’s MI6, was controlling Ukraine and turning it into a staging ground for operations against Moscow.

But the Times investigation found that Mr. Putin and his advisers had misunderstood a crucial dynamic. The CIA did not force its way into Ukraine. American officials were often reluctant to engage fully, fearing that Ukrainian officials could not be trusted and fearing to provoke the Kremlin.

However, a narrow circle of Ukrainian intelligence officials were assiduously courted by the CIA and gradually became vital to the Americans. In 2015, General Valeriy Kondratiuk, then head of Ukraine’s military intelligence, came to a meeting with the deputy chief of the CIA and handed over a stack of top-secret files without warning.

This first stack contained secrets of the Russian Navy’s Northern Fleet, including detailed information on the latest designs of Russian nuclear submarines. Soon, groups of CIA officers began regularly leaving his office with backpacks full of documents. General Kondratiuk said:

We understood that we needed to create the conditions of trust.

As the partnership deepened after 2016, the Ukrainians grew impatient with what they saw as Washington’s excessive caution and began organising assassinations and other deadly operations that violated the terms the White House believed the Ukrainians had agreed to. Angry officials in Washington threatened to cut off support but never did. A former senior US official said:

The relationships only got stronger and stronger because both sides saw value in it, and the US Embassy in Kyiv — our station there, the operation out of Ukraine — became the best source of information, signals and everything else, on Russia. We couldn’t get enough of it.

The CIA’s partnership in Ukraine can be traced back to two phone calls on the night of 24 February 2014, eight years before the military conflict began, according to The New York Times.

Millions of Ukrainians had just overthrown the country’s pro-Kremlin government, and President Viktor Yanukovych and his associates had fled to Russia. In the turmoil, a fragile pro-Western government quickly took power.

Valentin Nalyvaichenko, the new head of the spy agency, arrived at the domestic intelligence headquarters and found a pile of smouldering documents in the courtyard. Inside, many computers had been wiped or infected with Russian malware. He said in an interview:

It was empty. No lights. No leadership. Nobody was there.

He went to his office and called the CIA branch chief and the local head of MI6. It was past midnight, but he summoned them to the building, asked for their help in rebuilding the agency from scratch and offered a three-way partnership. Nalyvaichenko added:

That’s how it all started.

The situation quickly became increasingly dangerous. Russia expanded its presence in Crimea. Rebellions erupted in the east and escalated into fighting. Ukraine was at war, and Mr. Nalyvaichenko asked the CIA for aerial images and other intelligence to help defend its territory.

As violence escalated, an unmarked US government plane landed at Kyiv airport with John O. Brennan, then director of the CIA, on board. He told Nalyvaichenko that the CIA was interested in developing relations, but only at a pace that suited the agency, according to US and Ukrainian officials.

The unknown question for the CIA was how long Nalyvaichenko and the pro-Western government would be around. The CIA has been burned before in Ukraine.

After the collapse of the Soviet Union in 1991, Ukraine gained independence and then found itself caught between competing political forces: those who wanted to remain close to Moscow and those who sought alliance with the West. During his previous tenure as head of the spy service, Mr. Nalyvaichenko had begun a similar partnership with the CIA, which dissolved when the country turned back towards Russia.

Now Mr. Brennan explained that to get CIA assistance, the Ukrainians had to prove they could provide valuable intelligence to the Americans. In addition, they had to clear the country of Russian spies, which abounded in the domestic spy agency SBU (The Russians quickly learned of Mr. Brennan’s supposedly secret visit. Kremlin agencies published a photoshopped image of the CIA director in a clownish wig and make-up).

Mr. Brennan returned to Washington, where President Barack Obama’s advisers were deeply concerned not to provoke Moscow. The White House drew up secret rules that infuriated the Ukrainians and that some in the CIA thought were handcuffs. The rules forbade intelligence agencies from providing Ukraine with any support that was “reasonably expected” to have lethal consequences, The New York Times reports.

The result was a delicate balance. The CIA had to strengthen Ukraine’s intelligence services without provoking the Russians. The red lines were never precisely defined, creating constant tension in the partnership.

In Kyiv, Mr Nalyvaichenko chose his long-time aide, General Kondratiuk, to head counterintelligence. They created a new paramilitary unit that was deployed behind enemy lines to conduct operations and gather intelligence that the CIA or MI6 could not provide them.

The unit, known as the Fifth Directorate, was staffed by officers born after Ukraine’s independence. General Kondratiuk said:

They had no connection with Russia. They didn’t even know what the Soviet Union was.

That summer, Malaysia Airlines Flight 17, flying from Amsterdam to Kuala Lumpur, exploded in midair and crashed in eastern Ukraine, killing about 300 passengers and crew members. The Fifth Directorate produced intercepted phone calls and other intelligence within hours of the crash that quickly placed responsibility on rebels in eastern Ukraine.

The CIA was impressed and for the first time made a serious commitment, providing members of the Fifth Directorate and two other elite units with secure communications equipment and specialised training. A former US official, referring to intelligence that could help them fight the Russians, said:

The Ukrainians wanted fish and we, for policy reasons, couldn’t deliver that fish. But we were happy to teach them how to fish and deliver fly-fishing equipment.

In the summer of 2015, Ukrainian President Petro Poroshenko shook up the interior service and put an ally in place of Mr. Nalyvaichenko, a trusted CIA partner. But the change opened up new possibilities, according to The New York Times.

The reshuffle put General Kondratiuk in charge of the country’s military intelligence service, known as the HUR, where he had started his career a few years earlier. This was the first example of how personal connections, rather than policy changes, deepened the CIA’s involvement in Ukraine.

Unlike the domestic agency, the HUR was authorised to gather intelligence outside the country, including in Russia. But the Americans saw no point in developing this agency because it provided no valuable intelligence on the Russians and because it was seen as a bastion of Russian supporters.

In an attempt to build confidence, General Kondratiuk arranged a meeting with his American counterpart from the Defence Intelligence Agency and handed him a bundle of classified Russian documents. But high-ranking DIA officials were suspicious and did not recommend closer ties. The general needed to find a more willing partner.

A few months earlier, while still working for an internal agency, General Kondratiuk had visited CIA headquarters in Langley, Virginia. At these meetings, he met a CIA officer with a jovial disposition and a bushy beard who was being touted as the next station chief in Kyiv.

After a long day of meetings, the CIA took General Kondratiuk to a Washington Capitals hockey game, where he and the arriving station chief sat in a luxurious box and loudly booed Alex Ovechkin, the team’s star player from Russia.

The station chief had not yet arrived when General Kondratiuk handed over classified documents about the Russian navy to the CIA and  the documents were sent to analysts at Langley. He said:

There’s more where this came from.

The analysts concluded that the documents were genuine, and after the station chief arrived in Kyiv, the CIA became General Kondratiuk’s main partner.

General Kondratiuk knew he needed the CIA to strengthen his own agency. The CIA believed the General could help Langley as well. It had difficulty recruiting spies in Russia because its employees were under strict surveillance. He said:

For a Russian, allowing oneself to be recruited by an American is to commit the absolute, ultimate in treachery and treason. But for a Russian to be recruited by a Ukrainian, it’s just friends talking over a beer.

The new station chief began regularly visiting General Kondratiuk, whose office was decorated with an aquarium where yellow and blue fish – Ukraine’s national colours – swam around a model of a sunken Russian submarine. The two became close, which improved relations between the two departments, and the Ukrainians gave the new station chief an affectionate nickname – Santa Claus, The New York Times reports.

In January 2016, General Kondratiuk flew to Washington for a meeting at Scattergood, an estate on CIA property in Virginia where the agency often hosts receptions for high-level guests. The agency agreed to help the HUR modernise and improve its ability to intercept Russian military communications. In exchange, General Kondratiuk agreed to share all raw intelligence with the Americans. Now the partnership was real.

Today, the narrow road leading to the secret base is framed by minefields set up as a line of defence within weeks of the outbreak of the military conflict. Russian missiles striking the base seemed to close it down, but just weeks later the Ukrainians were back.

With money and equipment provided by the CIA, brigades under General Dvoretsky began to rebuild the base, but underground. To avoid detection, they worked only at night and when there were no Russian spy satellites overhead. The workers also parked their vehicles at a distance from the construction site.

In the bunker, General Dvoretsky pointed to communications equipment and large computer servers, some of which were funded by the CIA. He said his teams were using the base to hack into the Russian military’s secure communications networks. General Dvoretsky told a Times reporter during the tour, adding that they also hack into Chinese and Belorussian spy satellites:

This is the thing that breaks into satellites and decodes secret conversations.

Another officer placed two newly released maps on the table as evidence of how Ukraine is tracking Russian activity around the world.

The first showed the routes of Russian spy satellites passing over central Ukraine. The second showed Russian spy satellites passing over strategic military sites – including a nuclear weapons production facility – in the east and centre of the US, The New York Times reports.

General Dvoretsky said the CIA began sending equipment in 2016, after a key meeting in Scattergood, supplying encrypted radios and devices to intercept classified enemy communications.

Beyond the base, the CIA also oversaw a training programme held in two European cities to teach Ukrainian intelligence officers how to convincingly assume false identities and steal secrets in Russia and other countries adept at ferreting out spies. The programme was called Operation Goldfish, which comes from a joke about a Russian-speaking goldfish who offers two Estonians wishes in exchange for their freedom.

The point of the joke was that one of the Estonians smashed the fish’s head with a rock, explaining that anything that spoke Russian could not be trusted. Soon the officers of Operation Goldfish were deployed to 12 new forward operating bases built along the Russian border. According to General Kondratiuk, from each base, Ukrainian officers operated networks of agents who gathered intelligence information on Russian territory.

CIA officers installed equipment at the bases to help gather intelligence, and identified the most experienced Ukrainian graduates of the Operation Goldfish programme and worked with them to reach potential Russian sources. These graduates then trained “sleeper agents” in Ukraine to launch guerrilla operations in the event of occupation.

It often takes years for the CIA to gain confidence in a foreign agency and begin conducting joint operations. With the Ukrainians, it took less than six months. The new partnership began to yield so much raw intelligence on Russia that it had to be sent to Langley for processing.

But the CIA had red lines. It was not supposed to help the Ukrainians conduct offensive lethal operations. A former senior US official said:

We made a distinction between intelligence collection operations and things that go boom.

That distinction didn’t endear the Ukrainians to them. At first, General Kondratiuk was annoyed when the Americans refused to provide satellite images from Russian territory. Soon after, he asked the CIA for help in planning a covert mission to send HUR commandos to Russia to plant explosive devices in railway depots used by the Russian military. If the Russian military tried to advance into new Ukrainian territory, the Ukrainians could detonate explosives to slow the Russian advance.

When the station chief briefed his superiors, they, in the words of one former official, “went crazy”. Mr. Brennan, the CIA director, called General Kondratiuk to make sure the mission was cancelled and that Ukraine was abiding by “red lines” prohibiting lethal operations.

General Kondratiuk cancelled the mission, but he also learned another lesson. He said:

Going forward, we worked to not have discussions about these things with your guys.

Late that summer, Ukrainian spies discovered that Russian forces were stationing attack helicopters at an airfield on the Crimean peninsula, possibly for a surprise attack.

General Kondratiuk decided to send a team to Crimea to plant explosives at the aerodrome and detonate them if Russia launched an attack.

This time he did not ask permission from the CIA. He turned to Unit 2245, a commando unit that received special military training from the CIA’s elite paramilitary group known as the Ground Division. The purpose of the training was to teach defensive techniques, but CIA officers realised that without their knowledge the Ukrainians could use the same techniques in offensive lethal operations.

At the time, the future head of Ukrainian military intelligence, General Budanov, was a rising star in Unit 2245. He was known for daring operations behind enemy lines and had deep ties to the CIA. The agency trained him and took the extraordinary step of sending him to Walter Reed National Military Medical Centre in Maryland for rehabilitation after he was shot in the right arm during fighting in the Donbass.

Dressed in Russian uniforms, then Lieutenant Colonel Budanov led the commandos across the narrow bay in inflatable boats, landing at night in Crimea. But there an elite unit of Russian special forces was waiting for them. The Ukrainians fought back and then retreated to the coastline, plunged into the sea and sailed for several hours towards Ukrainian-controlled territory, The New York Times reports.

It was a disaster. In his public remarks, President Putin accused the Ukrainians of plotting a terrorist attack and vowed to avenge the deaths of the Russian fighters. He said:

There is no doubt that we will not let these things pass.

In Washington, the Obama White House was furious. Joseph R. Biden Jr. then vice president and a proponent of aid to Ukraine, called the president to complain angrily. He said in the call, a recording of which was leaked and published online:

It causes a gigantic problem. All I’m telling you as a friend is that my making arguments here is a hell of a lot harder now.

Some of Mr. Obama’s advisers wanted to shut down the CIA programme, but Mr. Brennan persuaded them that would be self-justifying, given that the relationship began yielding intelligence on the Russians while the CIA was investigating Russian interference in the election. Mr. Brennan contacted General Kondratiuk by telephone to reiterate the red lines.  He responded, according to a colleague:

This is our country. It’s our war, and we’ve got to fight.

The blow from Washington cost General Kondratiuk his job. But Ukraine did not back down.

A day after General Kondratiuk was ousted, a mysterious explosion ripped apart a lift in the Russian-controlled city of Donetsk in eastern Ukraine, carrying a high-ranking Russian rebel commander, Arsen Pavlov, known by the pseudonym Motorola, according to The New York Times.

The CIA soon learned that the assassins were members of the Fifth Directorate, a CIA-trained spy group. Ukraine’s domestic intelligence agency even handed out commemorative patches to the participants, each with the word “Lift” – the British term for a lift – written on it.

Again, some of Mr. Obama’s advisers were furious, but they were a “lame duck” – the presidential election, in which Donald Trump will battle Hillary Clinton, was three weeks away – and the killings continued.

A team of Ukrainian agents had set up an unmanned shoulder-fired rocket launcher in a building in the occupied territories. It was located directly across the street from the office of a rebel commander named Mikhail Tolstykh, better known as Givi. US.and Ukrainian officials said they fired the launcher as soon as Givi entered his office and killed him.

The shadow war raged with renewed vigour. The Russians used a booby-trapped car to kill the head of Unit 2245, an elite Ukrainian special forces unit. The commander, Colonel Maxim Shapoval, was on his way to a meeting with CIA officers in Kyiv when his car exploded.

At the colonel’s wake, US Ambassador to Ukraine Marie Yovanovitch stood in mourning next to the CIA station chief. Later, CIA officers and their Ukrainian counterparts toasted Colonel Shapoval with a shot of whiskey each. General Kondratiuk said:

For all of us, it was a blow.

The election of Mr. Trump in November 2016 put Ukrainians and their CIA partners on edge. Mr. Trump praised Mr. Putin and rejected Russia’s role in meddling in the election. He was suspicious of Ukraine and later tried to pressure its president, Volodymyr Zelensky, to investigate his Democratic rival, Mr. Biden, leading to Mr. Trump’s first impeachment.

But no matter what Mr. Trump says or does, his administration has often acted in the other direction. That is because Mr. Trump has appointed Russia hawks to key posts, including Mike Pompeo as CIA director and John Bolton as national security adviser. They visited Kyiv to underline their full support for the covert partnership, which has expanded to include more specialised training programmes and the construction of additional secret bases.

The base in the forest has grown to include a new command centre and barracks, and the Ukrainian intelligence staff has increased from 80 to 800. Preventing Russian interference in future US elections was one of the CIA’s top priorities during this period, and Ukrainian and US intelligence officers joined forces to probe the computer systems of the Russian intelligence services to identify operatives attempting to manipulate voters.

In one joint operation, the HUR team tricked a Russian military intelligence officer into providing information that allowed the CIA to link the Russian government to the so-called Fancy Bear hacking group, which has been linked to attempts to interfere in elections in a number of countries.

General Budanov, whom Mr. Zelensky appointed to head the HUR in 2020, said of the partnership:

It only strengthened. It grew systematically. The cooperation expanded to additional spheres and became more large-scale.

The relationship was so successful that the CIA wanted to replicate it with other European intelligence agencies focused on countering Russia.

The head of Russia House, the CIA division overseeing operations against Russia, organised a secret meeting in The Hague. At the meeting, representatives of the CIA, Britain’s MI6, the GID, the Dutch service (a crucial intelligence ally) and other agencies agreed to start pooling more intelligence on Russia. The result was a secret coalition against Russia – and the Ukrainians were its most important members.

In March 2021, the Russian military began massing troops along the border with Ukraine. As the months passed and more troops surrounded the country, the question arose whether Mr Putin was making a feint or preparing for war.

In November of that year and in the weeks that followed, the CIA and MI6 conveyed a single message to their Ukrainian counterparts: that Russia was preparing for a military conflict that would result in it wanting to expand its influence in Ukraine.

According to US officials, American and British intelligence agencies had intercepted material to which Ukrainian intelligence agencies did not have access. The new intelligence included the names of Ukrainian officials the Russians planned to kill or capture, as well as Ukrainians the Kremlin hoped to put in power.

President Zelensky and some of his advisers were not convinced, even after the CIA director, Mr. Burns, arrived in Kyiv in January 2022 to brief them.

As the outbreak of military conflict approached, CIA and MI6 officers made final visits to Kyiv to their Ukrainian counterparts. One M16 officer wept in the presence of the Ukrainians, fearing the Russians would kill them.

At Mr. Burns’ insistence, a small group of CIA officers were exempted from the wider US evacuation and moved to a hotel complex in western Ukraine. They did not want to leave their partners behind.

After the military conflict in Ukraine began on 24 February 2022, the CIA officers at the hotel were the only US government representative on the ground. Every day at the hotel, they met with their Ukrainian contacts to pass on information. The old handcuffs were removed and the Biden White House authorised spy agencies to provide intelligence support for lethal operations against Russian forces in Ukraine, The New York Times reports.

Often CIA briefings contained shocking details. On 3 March 2022 – the eighth day of the war – the CIA team gave a precise overview of Russian plans for the next two weeks. On the same day, the Russians would open a humanitarian corridor from besieged Mariupol.

According to the CIA, the Russians planned to surround the strategically important port city of Odessa, but a storm delayed the assault and the Russians never took the city. When the Russian offensive on Kyiv stalled, the head of the CIA got excited and told his Ukrainian counterparts that they were “punching the Russians in the face,” according to a Ukrainian officer in the room.

A few weeks later, the CIA returned to Kyiv, and the agency sent dozens of new officers to help the Ukrainians. One senior US official said of the CIA’s significant presence:

Are they pulling triggers? No. Are they helping with targeting? Absolutely.

Some of the CIA officers were sent to Ukrainian bases. They studied lists of potential Russian targets the Ukrainians were preparing to strike, comparing the information the Ukrainians had with US intelligence to make sure it was accurate.

Before the conflict, the CIA and MI6 trained their Ukrainian counterparts to recruit sources and set up clandestine and guerrilla networks. According to General Kondratiuk, in the southern Kherson region, which was under Russian control in the first weeks of the war, these guerrilla networks went into action, killing local collaborators and helping Ukrainian troops strike Russian positions.

In July 2022, Ukrainian spies spotted Russian columns preparing to cross a strategic bridge over the Dnieper River and notified MI6. British and American intelligence quickly verified the Ukrainian information using real-time satellite imagery. MI6 relayed the confirmation and the Ukrainian military fired rockets, destroying the convoys.

In an underground bunker, General Dvoretsky reported that a German anti-aircraft system now protects against Russian attacks. An air filtration system protects against chemical weapons, and a special power supply system is in place in case of a power failure.

Some Ukrainian intelligence officials are now asking their American counterparts – while Republicans in the House of Representatives decide whether to cut off billions of dollars in aid – whether the CIA will abandon them. One senior Ukrainian officer said:

It happened in Afghanistan before and now it’s going to happen in Ukraine.

Speaking about Mr. Burns’ visit to Kyiv last week, a CIA spokesman said:

We have demonstrated a clear commitment to Ukraine over many years and this visit was another strong signal that the US commitment will continue.

The CIA and the HUR have built two more secret bases to intercept Russian communications, and combined with the 12 forward operating bases that General Kondratiuk said are still operational, the HUR is now collecting and producing more intelligence information than it ever did during the war – much of it shared with the CIA. General Dvoretsky said:

You can’t get this kind of information anywhere else – only here and now.

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