The Iraqi army, supported by Iranian-backed Shiite militias known as Popular Mobilization Units (PMU), bloodlessly moved into the disputed areas of Khanaqin near the border with Iran and Sinjar and Bashiqa in Nineveh province after Kurdish peshmerga forces withdrew.
Iraq's Prime Minister Haidar al-Abadi reiterated that Iraqi forces had taken over the disputed areas from the Kurds with barely a shot fired. "I call on our citizens to celebrate this day, because we have been united," al-Abadi said.
He called the independence vote "a thing of the past" and offered to start talks with the Kurdish regional government.
The United States, which has provided arms and training to both the Iraqi army and peshmerga, has urged both sides to de-escalate the situation. President Donald Trump said that the US would "not take sides."
Iraq recaptures Sinjar
In Sinjar, a Yezidi militia called Lalesh, which is tied to the government in Baghdad, moved in to control the area after Kurdish forces retreated without a fight.
Sinjar is home to the small Yezidi religious community that faced genocide in August 2014 when the "Islamic State” (IS) group advanced through the area after Kurdish forces fled, prompting a US military intervention.
Peshmerga tied to Kurdish President Masoud Barzani retook Sinjar from IS in an offensive in late 2015, in a move that further expanded Kurdish control over territories claimed by the central government.
But many Yezidis, who speak Kurdish, looked on coldly at Barzani's Kurdistan Democratic Party (KDP), blaming it for the massacre, rape and slavery of Yezidis at the hands of IS following the peshmerga's previous withdrawal.
Referendum stokes tensions
The Kurds control three provinces in northern Iraq that make up the constitutionally recognized autonomous Kurdistan region. But they nearly doubled territory under their control since June 2014, when the Iraqi army collapsed during an IS advance through large swaths of Iraq.
With IS losing much of the territory it captured during its 2014 military assault, Baghdad and the Kurds' common fight against the extremists has taken a backseat and tensions over disputed territories have re-emerged.
The Kurds held a nonbinding independence referendum last month passed by more than 90 percent of voters, but it was held despite opposition from some Kurdish parties.
Controversially, the vote also included so-called disputed areas outside the KRG's official boundaries, including Kirkuk.
Baghdad viewed the referendum as unconstitutional and vowed to reassert control over disputed territories.
The US, UN and EU had opposed the vote. Turkey and Iran, fearful of Kurdish separatism in their countries, have responded by aligning with Baghdad against the Kurds.
Iraqi government seizes Kirkuk
Iraq's Prime Minister Haidar al-Abadi ordered troops and PMU forces to retake Kirkuk on Monday, seizing oil fields, government buildings and reasserting control over the province inhabited by Kurds and Sunni and Shiite Arabs, as well as a small Christian community.
Peshmerga fled north, with only minor clashes reported.
Overnight, the green, red and white Kurdish flags with a blazing yellow sun were taken down across Kirkuk, dashing with it Kurdish dreams of independence.
For the Kurds, control of Kirkuk would have helped underpin political independence through economic control of the province's oil and gas resources.
The Kurds export an average of 600,000 barrels of oil per day, of which 250,000 came from the three fields they controlled in Kirkuk province.
Their loss will add strain to the Kurdistan region's already dire economic and financial crisis, which has left peshmerga and civil servants either unpaid or partially paid.
The loss of Kirkuk has opened up long simmering intra-Kurdish feuds. The KDP has accused its main rival, the Patriotic Union of Kurdistan (PUK), of "treason" for abandoning Kirkuk.
Each party has separate peshmerga forces in control of fiefdoms in the east and west of the Kurdistan region, raising concern their power struggle could unleash a Kurdish civil war. The two parties fought a four-year civil war in the 1990s.
Barzani, in his first statement since the fall of Kirkuk, blamed the withdrawal from Kirkuk on "certain individuals in certain political parties," in a reference to the PUK. However, he did not mention that his KDP units also withdrew.
The PUK and the second-largest party in the Kurdish parliament, Gorran, accuse Barzani of holding the independence referendum to increase his power and grab Kirkuk, which was under the control of the PUK. They also accuse the Barzani family of wasting Kurdistan's oil wealth through party- and clan-based corruption.
"While we were occupied with protecting the Kurdish people, Barzani was hustling to steal petrol and reinforce his influence," said Lahour Sheikh Zengi, the head of the PUK's counterterrorism force. "From now on we are not going to sacrifice our sons for the sake of Barzani's throne."
But some factions within the PUK viewed Karim as too close to the KDP, suspecting that in the wake of the referendum he would help the KDP control Kirkuk.
The PUK, whose Fuad Masum is Iraq's president, is close to Iran and is more amenable to negotiations with Baghdad.
On Tuesday, he blamed Barzani's insistence on unilaterally holding the referendum for the current crisis with the central government and the loss of Kirkuk.
"Holding a referendum on the Kurdistan region's independence from Iraq stirred grave disagreements between the central government and the government of Kurdistan," he said in a televised address, adding that this "led to federal security forces retaking direct control of Kirkuk."
Gorran and the PUK are now calling for a caretaker government to be formed to negotiate with Baghdad, Barzani to resign and new elections to be held. Barzani's term expired in 2013, but was controversially extended.
The Kurdish parliament has not held a full session since 2015, when four Gorran ministers were sacked from the Cabinet and the KDP blocked Gorran's parliamentary speaker from the capital, Irbil.
The Kurdistan region is supposed to hold parliamentary and presidential elections in November, but the latest intra-Kurdish conflict and the situation with Baghdad now casts doubt over whether they will be held.