Afghanistan War (2001-), major combat phase
As part of the United States Central Command's (CENTCOM) Operation ENDURING FREEDOM plan, after infrastructure and special operations forces were established, the U.S. would assist Afghan ground forces in decisive combat operations against the Taliban and al-Qaeda. U.S. ground forces took a minimal role in this phase, although air and special operations forces were extremely active.
There was not a unified Afghan resistance command. The largest single group was the Northern Alliance, although an ad hoc Eastern Alliance formed for the Battle of Tora Bora. Some independent militias operated in other areas. After the capture of Kabul and the establishment of an interim national government, there was a greater degree of coordination.
On October 30, GEN Tommy Franks, commanding CENTCOM, met with Mohammed Fahim Khan of the Northern Alliance and Gary Berntsen of the CIA. Franks set out his priorities: have the Northern Alliance forces of Dostum take the major Northern city of Mazar-e-Sharif, use it as a staging area to make a joint attack with Uzbek forces, now under Berryelah Khan, to make a joint attack on Taloquan. Taking those cities would open an overland supply route to Uzbekistan. According to Bertsen, Franks wanted Fahim's forces, farther south on the Shomali Plain, to move west and cut off the escape of the Taliban in the north. Fahim argued that he wanted to move to take Kabul first. Bertsen saw Fahim's argument as political; Franks restated his plan of Mazar-e-Sharif, Taloquan, and the Shomali Plains.
Once the northern cities were taken, Franks wanted the The Northern Alliance would then to take Bagram Air Base, and then go from the Panshjir Valley to the Shomali Plain north of Kabul. He did not state Fahim's argument for Kabul as strongly as did Bertnsen. Fahim agreed not to enter Kabul without Franks' permission; Franks and the CIA supported Hamid Karzai, a Durrani Pashtun as the interim national leader, and did not want tribal conflict between Pashtuns and the Northern Alliance tribes. A day or two later, Berntsen and a Special Forces team talked to Fahim's forces on the Shomali Plain, and told them they could not have more airstrikes that were needed in the north.
There is a widespread but incorrect impression that the Northern Alliance had extensive close air support as soon as the Special Forces teams joined them. The reality was that while there was an extensive bombing campaign, it initially focused on suppression of enemy air defense (SEAD) and objectives that the United States believed were strategic, such as Taliban infrastructure. Close air support was essentially on an as-available basis until the movement to take Kabul; it became much more available from that time onwards.
While plans were fairly specific through the capture of Kabul, they became more ad hoc from that point onwards, especially in the pursuit of al-Qaeda and Taliban leadership. The relationship of Pakistan, and to a lesser extent other surrounding countries, changed in the aftermath of Kabul.
Air attacks had started on October 7, but depended on U.S. remote sensing rather than on-the-ground fire direction. While CIA teams were in the country, they were not allowed to direct strikes; that was a Special Forces responsibility, starting in mid-October. The key campaign plan came out of the October 30 meeting with Franks and Fahim.
Northern regional campaign
The attack on Mazir-e-Sharif began on November 5; it was captured on November 10. The battle was a series of probes, by Northern Alliance horse cavalry until Taliban resistance was met, and then the Special Forces team called in air strikes. Cavalry charges immediately following airstrikes, if a mix of the centuries, were effective.
Taloqan soon followed, as did Herat and Shindand in the east. 
President George W. Bush, on November 7, said "We will encourage our friends to head south across the Shomali Plains, but not into the city of Kabul itself." On November 8, Special Forces and CIA personnel were on the Shomali Plains, waiting for air support so that the Northern Alliance could advance against an estimated 10,000 Taliban.British Special Boat Service personnel joined U.S. special operators to seize Bagram Air Base outside Kabul on November 11. According to Berntsen, on the 12th, "Kabul is reported to be in a state of confusion. The Taliban are withdrawing. We need to move quickly in order to receive maximum benefit from our enemy's retreat." Bismullah Khan's force, accompanied by Special Forces ODA 555, advanced rapidly. ODA 555 was aware of the agreement between Mohammed Fahim Khan and GEN Franks, but, as a team member put it,
General Sharifi [a subcommander of Bismullah Khan who was the main ODA 555 contact] was like, "Sure we'll stop," and he goes, "But you know, some of the local commanders have family down there," and he kind of let it known that they weren't going to stop. Politically, yes, you know we were going to stop. [But] if a guy is trying to get back to his old home in Kabul, then who's going to stop them? They're not going to stop them, and that's what ended up [happening]. [Some people were asking], "[Were] there gangs running around Kabul?" Someone had to go in there and secure it to make it safe for the people. So that's why they went in.
The Northern Alliance violated an agreement not to take Kabul until an international peacekeeping force was ready. They took control of Kabul on November 13. Pakistan's leader had called for it to be a "demilitarized city", and referred to the previous bloody takings of Kabul by the Northern Alliance in 1992 and by the Taliban in 1996.
Bin Laden was observed in Jalalabad on the 12th, and seen moving southeast toward the Pakistani border on the 14th. CIA personnel knew he had had a training camp at Tora Bora, and a network of caves above it; they expected him to move to Tora Bora.
After Kabul fell, a Combined Air Operations Center (CAOC) officer observed “we sat there with report after report after report of thousands of vehicles leaving Kabul” on the southwestern road leading to the Khost-Gardez region. Due to concern over civilian casualties, they were not aggressively prosecuted with air strikes. On the 16th, however, the CIA received confirmation that Mohammed Atef, the al-Qaeda military commander, was killed in an airstrike outside Gardez on the 1tht. 
Heavy fighting, however, continued. Kunduz continued to resist, as did Kandahar.
A preparatory step before taking Kandahar was taking Tarin Kowt. In the latter engagement, Hamid Karzai was among the fighters; the Taliban sent a strong force to stop him. Special Forces ODA 574, commanded by CPT Jason Amerine, joined him, on November 14. The A-team infiltrated through Oruzgan Province to link with Karzai, who had said Tarin Kowt, even more than Kandahar, was the main area from which the Taliban leadership came. Mullah Omar, for example, was from Deh Rawod, which was just to the west of Tarin Kowt. 
Two days later, 500 Taliban fighters were moving against Karzai's force, which had 30-60 Afghans and 11 Special Forces soldiers. The force received extremely effective close air support, leaving only three pickup trucks of Taliban to be fought directly.
Karzai told Amerine that this was the decisive psychological victory of the war. He had been concerned that the local mullahs would tell him to leave with the Americans, but, instead, they said "'If the Americans hadn't been here, we all would have been killed,' meaning the reprisal against them for what had happened and the uprising in the first place."
As they moved toward Kandahar, intense fighting was taking place at Kunduz.
Kunduz was surrounded from three sides: Mazar-e-Sharif in Balkh Province to the west, Taloqan in Takhar Province on the east, and Pul-e-khumri in Baghlan Province to the south. Negotiations for its surrender took place at Emam Sahib on November 15. As many as 20 separate Afghan Taliban leaders were involved, each with his own following. Complicating the situation is that while the Northern Alliance would usually accept the surrender of Afghans, it often gave no quarter to foreign fighters. 
Afghan Taliban fighters surrendered at Kunduz, but foreign fighters, including Juma Namangami, a leader of the Islamic Movement of Uzbekistan, fought on. Namangami led the al-Qaeda force at Kunduz, and was killed in a U.S. airstrike; the overall Taliban commander was Mohammed Fazal. 
Kunduz fell on November 23-24; 8,000 Taliban surrendered. Amir Jhan, a former Taliban apparently accepted as a negotiator by both sides, said that after the surrender, he counted only 3,015. There are many theories for prisoner deaths, ranging from compounded errors to deliberate killing; there appear to have been miscalculations on all sides.
When the Taliban evacuated Kabul, they called for guerrilla resistance, but still put on a static defense at Kandahar. As Karzai and ODA574 approached from the north, another anti-Taliban force, under Gul Agha Sharzai, the former governor of Kandahar, assisted, from November 13, by Special Forces ODA 583, was moving to Kandahar from the south. U.S. Marines were approaching from the southwest.
LTC David Fox, commanding the Special Forces battalion that controlled the ODAs, joined Karzai on November 28, to become Karzai's military adviser and Special Forces C detachment commander, letting the ODA go back to tactical operations. Fox said Karzai did not have direct military experience, but immense intelligence and political skills. In late November, air attacks forced the Taliban out of Takrit-e Pol, which was then taken by Sharzai's force. Taking the town gave them control of the Spin Boldak-Kandahar highway. From there, they set up an observation post near Kandahar Airfield, from which airstrikes were directed for a week.
The Taliban made a brief stand against Karzai on December 3, but retreated. On December 5, however, ODA 574 and Karzai suffered the worst fratricide ("friendly fire") incident of the war. An air controller replaced the batteries in the instrument used to direct bombs. When the device was restarted, it would send its own position until a new target was designated, which did not happen. Bombs hit their position, killing 30 and wounding many more.
At this point, the key CIA briefer to Bush and Cheney was Hank Crumpton, who was the head of the Afghanistan operations at CIA headquarters. Crumpton, in advice described as above his pay grade, urged that Marines or other troops move to Tora Bora; the Afghan allies were not up to the job.
On December 6, Northern Alliance leaders, including Karzai, met with Taliban leaders and negotiated a surrender of the city. Some Taliban put down their weapons, while others moved into guerrilla warfare.
Karzai had been moving to attack the airfield on the 7th, but learned of the surrender terms negotiated by Karzai, and moved to take the town without fighting. Karzai reconfirmed him as governor. 
Tora Bora is an extremely rugged area, south of Jalalabad, as having two valleys running north and south. One U.S. soldier called it a "vertical no man's land, a hellish place of massive, rocky, jagged unforgiving snow-covered ridgelines and high peaks separated by deep ravines and valleys studded with mines.  It is believed that bin Laden and his key supporters fled there after Jalalabad fell, and eventually escaped to Pakistan. There is much controversy over the policies and tactics with which the battle was fought, involving decisions up to the level of the U.S. President. Tactical command is also an issue; at the very least, both the Joint Special Operations Command Special Mission Unit under BG Gregory Trebon, USAF, and the 5th Special Forces Group, under COL John Mulholland, U.S. Army, were involved. If the Pakistani border were to be blocked, more ground troops would have been needed. Both GEN Tommy Franks and MG Dell Dailey were advising.
There was considerable argument, up to the Presidential level, on how to proceed against Tora Bora, where bin Laden had been identified. CIA had proposed putting American troops on the Pakistan side of Tora Bora, saying Pakistan could not contain bin Laden. President Bush, according to Suskind, decided to trust Pakistan.  As an alternative, it had been proposed to mine the passes leading out of Tora Bora, but some U.S. allies had said they would leave the coalition if mines were used.  GEN Franks said he was pleased with the operation and was not sure bin Laden had been there. Other Americans, however, believed “because there were not enough boots on the ground, that some bad guys got away. The way to rectify that was to increase the became the later concept for Operation ANACONDA in the Shahi-i-Khot Valley.
A large concentration of Taliban and al-Qaeda was identified in the Shah-i-Khot Valley of Paktia Province southeast of Gardez, which was reported to Advanced Force Operations (AFO) on January 15. While attacking with Afghan forces assisted by Special Forces was considered, the size of forces there indicated that conventional forces might be needed. Planning of Operation ANACONDA (Afghanistan War 2001-) was taken on the 10th Mountain Division on 15 February. Eventually the force would have 1000 Afghan troops with United States Army Special Forces, personnel from Joint Special Operations Command, and a U.S. infantry brigade. They would form three concentric circles around the valley, cutting off escape routes before the main attack. This was to be the first sustained battle by U.S. ground troops.
A motto of the U.S. military is "train like you fight; fight like you train." This clashed, especially at Shah-i-Kot, when Rumsfeld and his staff limited the forces that could go into Afghanistan. In particular, they were told to limit force size by not bringing the artillery that was normally part of combat units. This left them without weapons that could engage enemy guns under overhanging cliffs, immune to air strikes. 
TF DAGGER, the 5th Special Forces Group, also made the area its first priority on January 20.  There were to be command problems throughout the operation. Originally, it was planned by Special Operations, but COL Mulholland realized a larger force was needed. MG Franklin L. “Buster” Hagenbeck, commanding the 10th Mountain Division, was put in charge of planning for Army elements. 
Air Force planners were not involved until February 23, although Special Operations had begun their planning on February 6.  The Air Force was critical of the lack of unified command, and the proper use of air assets. The Army originally expected fairly light resistance, but Khost was already starting to show enemy concentrations.
The 10th Division, however, did not have its full planning staff, nor did it have clear authority over other components until CFLCC issued Fragmentary Order 2 to. Operations Order 02–018 (“Establishment of CJTF MOUNTAIN”); the date is uncertain but probably was February 25th. 
The active battle ran from March 2 to 16,  although troops began to set blocking positions on February 26. The first troops into the area were U.S. and Australian special operations forces infiltrated three days before the main attack, from JSOTF-S/Task Force K-BAR. Their mission was special reconnaissance (SR) for surveillance and fire control. day for forces introduced on Takur Ghar, a peak overlooking the area.
On March 1st, Task Force ANVIL, consisting of 600 Afghan militia led by Special Forces, took blocking positions on lines of escape, and then a U.S. task force, from the 101st and 10th divisions, would make an air assault to an inner line of blocking positions on the east of the valley. On the 2nd, Task Force HAMMER, of 260 Afghan and Special Forces troops, attacked into the center of the Taliban position. This was the plan, but it broke down under heavy fire. 
To retrieve the situation, more SR forces were needed, and U.S Navy SEALs were to be put on Takur Gar. Seven of U.S. deaths came on 4 March 2002 at the ridgeline at Takur Gar, when a helicopter insertion of special operations forces, and a rescue attempt, ran into serious trouble. As a U.S. Navy SEAL team was being landed, their helicopter was hit by a rocket-propelled grenade, and Petty Officer Neil C. Roberts fell from the aircraft. The lead CH-47 from a rescue force was also hit by RPG fire and crashed. In spite of massive close air support, some special operations forces were overcome. 
As of March 3, the higher command allowed the TF Rakkasan reserve battalion to be committed, but also to let mortar, artillery and air strikes take up more of the load, keeping the Army troops more static. They did find the 120mm mortar to be surprisingly effective in mountain combat.
Another reason was to give the Afghan troops pride and experience. LTC Jim Larsen, TF Rakkasan's executive officer, said "We could have taken that town [Serkhankhel] any time we wanted to, but that would not have helped in the overall purpose of legitimizing that [Afghan]] military." Negotiations between the warlords, however, was frustrating to the Americans and made coordination almost impossible. They were, however, impressed with the leadership of Gul Haider.
- Gary Bertsen and Ralph Pezzulo (2005), JAWBREAKER: The attack on Bin Laden and al-Qaeda: A Personal Account by the CIA's Field Commander, Three Rivers Press, Crown Publishing Group, Random House, ISBN 0307351068, pp. 90-92
- Tommy Franks (2004), American Soldier, Harper Collins, ISBN 0060779543, p. 310-312
- Gary C. Schroen (2005), First In: An Insider's Account of How the CIA Spearheaded the War on Terror in Afghanistan, Ballentine, ISBN 0891418723, pp. 240-241
- "Operation Enduring Freedom - Operations", Globalsecurity
- Berntsen, p. 164
- Interview: U.S. Special Forces ODA 555, Frontline, Public Broadcasting Service
- Rupert Cornwell (November 14, 2001), "West tries to put brave face on Kabul's capture", Independent (U.K.)
- Berntsen, p. 239
- Operation Anaconda: An Air Power Perspective, U.S. Air Force, 2005, p. 17
- Berntsen, p. 206
- History 1987-2007, United States Special Operations Command, p. 93
- "Interview: U.S. Army Captain Jason Amerine", PBS Frontline, July 9 and 12, 2002
- Dexter Filkins (November 15, 2001), "A NATION CHALLENGED: THE HOLDOUTS; Taliban Negotiating Surrender of Kunduz, Their Last Stronghold in Afghanistan's North", New York Times
- Berntsen, p. 242
- "Interview: Lt. Col. David Fox", PBS Frontline
- Ron Suskind (2006), The One Percent Doctrine: Deep Inside America's Pursuit of its Enemies Since 9/11, Simon and Schuster, ISBN 9780743271097, pp. 57-59
- USSOCOM History, p. 94
- Dalton Fury (pseud.) (2008), Kill Bin Laden: a Delta Force Commander's Account of the Hunt for the World's Most Wanted Man, St. Martin's Press, ISBN 0312384394, p. 74
- Ron Suskind, The One Percent Doctrine, p. 74
- Fury, p. 78
- Air Power Perspective, p. 19
- Sean Naylor (2005), The untold story of Operation Anaconda: Not a Good Day to Die, Berkley, ISBN 0425196097, p. 40
- Thomas E. Ricks (2006), FIASCO: the American Military Adventure in Iraq, Penguin, ISBN 159320103X, p. 41
- Naylor, pp. 42-43
- USSOCOM History, p. 98
- Air Power Perspective, p. 8
- Richard L. Kugler, Michael Baranick, and Hans Binnendijk (March 2009), Operation Anaconda: Lessons for Joint Operations, Center for Technology and National Security Policy, National Defense University, p. 2
- Dexter Filkins, James Dao (March 19, 2002), "A NATION CHALLENGED: THE FIGHTING; Afghan Battle Declared Over And Successful", New York Times
- USSOCOM history, pp. 98-100
- Air Power Perspective, pp. 75-80
- Naylor, pp. 369-373