General Wavell's political connections in Britain and patronage (he admired Wingate's work in the Abyssinian campaign) protected Wingate from closer scrutiny. In the jungle, he grew a beard and allowed his men to do the same, but by his outstanding courage and leadership in the face of the enemy, won plaudits. The original 1943 Chindit operation was supposed to be a coordinated plan with the field army. When the offensive into Burma by the rest of the army was cancelled, Wingate persuaded Wavell to be allowed to proceed into Burma anyway, arguing the need to disrupt any Japanese attack on Sumprabum as well as to gauge the utility of long-range jungle penetration operations. Wavell eventually gave his consent to Operation Longcloth.

Wingate set out from Imphal on 12 February 1943 with the Chindits organized into eight separate columns to cross the Chindwin river. The force met with initial success in putting one of the main railways in Burma out of action. Afterwards, Wingate led his force deep into Burma and then over the Irrawaddy river. Once the Chindits had crossed, they found conditions very different from that suggested by the intelligence they had received. The area was dry and inhospitable, criss-crossed by motor roads which the Japanese were able to use to good effect, particularly in interdicting supply drops to the Chindits who soon began to suffer severely from exhaustion and shortages of water and food.

On 22 March, Eastern Army HQ ordered Wingate to withdraw his units back to India. Wingate and his senior commanders considered a number of options to achieve this but, all were threatened by the fact that with no major army offensive in progress, the Japanese would be able to focus their attention on destroying the Chindit force. Eventually they agreed to retrace their steps to the Irrawaddy, since the Japanese would not expect this, and then disperse to make attacks on the enemy as they returned to the Chindwin. By mid-March the Japanese had three infantry divisions chasing the Chindits, who were eventually trapped inside the bend of the Shweli River by Japanese forces. Unable to cross the river intact and still reach British lines, the Chindits was forced to split into small groups to evade enemy forces. The Japanese paid great attention to preventing air resupply of Chindit columns, as well as hindering their mobility by removing boats from the Irrawaddy, Chindwin and Mu rivers and actively patrolling the river banks. Continually harassed by the Japanese, the force returned to India by various routes during the spring of 1943 in groups ranging from single individuals to whole columns: some directly, others via a roundabout route from China. Casualties were high; the force lost approximately one-third of its total strength.

While Wingate was still in Burma, Wavell had ordered the formation of 111 Brigade, known as the "Leopards", along the lines of the 77 Brigade. He selected Brigadier Joe Lentaigne as the new commander. Wavell intended that the two brigades would operate with one engaged on operations while the other trained and prepared for the next operation. However, once back in India, Wingate was promoted to acting major general and was given six brigades. This involved breaking up the experienced 70th Division, which other commanders felt could be better used as a standard "line" division. At first, Wingate proposed to convert the entire front into one giant Chindit mission by breaking up the whole of the Fourteenth Army into Long-Range Penetration units, presumably in the expectation that the Japanese would follow them around the Burmese jungle in an effort to wipe them out. This plan was hurriedly dropped after other commanders pointed out that the Japanese Army would simply advance and seize the air bases from which Chindit forces were supplied, requiring a defensive battle and substantial troops that the Indian Army would be unable to provide.

In the end, a new long-range jungle penetration operation was planned, this time using all six of the brigades recently allocated to Wingate. The second long-range penetration mission was originally intended as a coordinated effort with a planned regular army offensive against northern Burma, but events on the ground resulted in cancellation of the army offensive, leaving the long-range penetration groups without a means of transporting all six brigades into Burma. Upon Wingate's return to India, he found that his mission had also been cancelled for lack of air transport.