The decision not to take Tripoli had serious consequences for the British. On February 12, 1941, General Erwin Rommel, newly appointed commander of Germany's Afrika Korps, arrived in Tripoli to help Italy get back what the British had taken. Though officially under an Italian general, Rommel, a savvy military strategist and gamesman, pretty much ran the show on his own. In March, after amassing a strong German-Italian force fortified with tanks and heavy artillery, Rommel headed to Cyrenaica. The small British force there was quickly overwhelmed by the German war machine, and by April Rommel had succeeded in retaking everything except Tobruk, where the British had set up a strong defense. Over the course of the campaign, Rommel managed to capture General O'Connor and two other generals who were sent to Italy as prisoners of war, but O'Connor escaped in December 1943.

By the end of his offensive, Rommel had crossed the border into Egypt, where he took Halfaya Pass. Having initially bypassed Tobruk, he returned to lay siege to the fortified port city. Wavell tried to break the German hold on Tobruk with two assaults, code-named Brevity and Battleax, but succeeded only in losing nearly half his armor to Rommel. The defeat was a serious problem for Winston Churchill, who had gone against his military advisers by taking tanks and fighter aircraft from Great Britain and giving them to Wavell. Churchill had no recourse but to replace Wavell with General Claude Auchinleck, who in November 1941 mounted another offensive against the Germans. His goal was twofold: Cover a breakout from Tobruk and recover the territory taken by Rommel.

The battle lasted until mid-December, when Auchinleck's army successfully lifted the siege of Tobruk and pushed Rommel all the way back to El Agheila. Both sides experienced heavy casualties, but the victory went to Auchinleck, who lost less of his military strength than did Rommel.

However, the German defeat did not mean the end of the war in North Africa. If anything, it only served to accelerate the action. Rommel's supply lines were far shorter than Auchinleck's, and his army was soon reinforced, resupplied, and rearmed. The situation might have been quite different had the RAF not been preoccupied supporting British forces in Malta.

On January 21, 1942, Rommel struck again against the British, this time with overwhelming force. He recaptured Benghazi (and the British arsenal stored there) and pressed to within 35 miles of the British stronghold at Tobruk. Startled by Rommel's strength, the British withdrew to the Gazala line, a series of defensive structures linked by minefields that ran from El Gazala on the coast to Bir Hacheim, approximately 40 miles southwest of Tobruk.

Rommel and Auchinleck paused to regroup and amass supplies. Auchinleck also used the time to reinforce the center of the Gazala line. On May 26, Rommel finally made his move, maneuvering swiftly around the southern end of the Gazala line in the hope of taking Bir Hacheim and then eliminating the defensive boxes one at a time. But things suddenly turned sour for Rommel, who found himself trapped between British bunkers and facing almost certain annihilation.

It was then that Rommel demonstrated his true skill as a military leader. Through sheer drive, he rallied his army to overrun Bir Hacheim, smash a series of British defensive boxes, then make a mad run for a large British supply dump east of Tobruk. Four days later, Rommel's Afrika Korps swarmed Tobruk, capturing the town and its huge cache of supplies — enough to supply 30,000 men for three months. The only thing denied Rommel was the British gasoline supply, which was set ablaze before the Germans could get to it.

Having lost Tobruk, the British regrouped and formed another defensive line at Mersa Matruh deep inside Egypt. Behind that was a last-ditch defense at El Alamein, which protected Alexandria. If that fell, so would Egypt.

Rommel, his reputation taking on almost legendary proportions, took Mersa Matruh at the end of June, then set his eyes on the El Alamein line, which stretched for 35 miles and was protected at the flanks by a series of natural obstacles that made access extremely difficult. The sea lay to the north of the line, and to the south was the Qattara Depression, nearly 7,000 square miles of terrain so harsh that it was virtually unpassable.

Adding to Rommel's woes were dwindling supplies, constant harassment by the RAF, and the fact that his men were exhausted after weeks in the desert. As a result, when Rommel's forces finally reached the El Alamein line on July 1, they lacked the strength and resources to smash through.