In late 49 BC, Caesar and his 12 legions arrived at Brundisium where he hoped to secure passage to Greece. An old rival, Bibulus, controlled the Ionium Sea with the Republican navy, and Caesar fretted over when and how to make a crossing. By January of 48 BC, Caesar decided there was no time like the present and decided to make a surprise winter crossing, to offset the advantage that the enemy maintained in naval superiority. Unfortunately, he could only secure enough transports for 7 depleted legions, or 15,000 men and about 500 cavalry, and after landing safely at Palaeste, he sent his ships back to Brundisium to transport Marcus Antonius and the remaining 5 legions. With the element of surprise gone after the first successful crossing, Bibulus got word of the return trip and intercepted Caesar's fleet. Blocked off by Bibulus, Antony and Caesar's remaining forces along with the bulk of the supplies were forced to wait near Brundisium.
Now isolated in Greece, Caesar and his much smaller army were in serious jeopardy. Pompey seriously outnumbered him, some 55,000+ to Caesars' 15,000, and Caesar was dreadfully low on supply. Caesar moved north from his landing position, first on Apollonia, then on Pompey's vital supply depot at Drryhachium. Pompey, however, was already on the move to the town where he planned to quarter his army for the winter. In the meantime, Caesar made an important diplomatic gesture to prevent war. Still probably fully intent on 'winning' on the battlefield, he could be sure, however, that any proposal for peace would be rejected. By sending Vibullius Rufus to negotiate, Caesar could claim to be the peacemaker and that Pompey and the Republicans were the real cause of the war. Regardless, Caesar moved his army to the south side of the Apsus River, while Pompey positioned his on the north bank. There the two armies waited out the winter months, while Pompey did nothing against his much smaller foe.
Over the course of the winter, Caesar was not idle. He and his men not only were busy foraging for food, but managed to turn the tables on Pompey's fleet. Bibulus and the fleet prevented supplies, and Antony's reinforcements from reaching Caesar, but Caesar's forces prevented the fleet from going into various ports to get re-supplied as well. By mid winter, Bibulus died from sickness and the Pompeian fleet was in as desperate shape as Caesar's army. On the ground, the situation seemed more like a reunion of soldiers than two opposing armies about to do battle. Pompey's men clearly feared Caesar, and despite their numerical superiority there seemed to be little will to fight. Fraternization among the men on both sides might have slowly eroded support for the idle Pompey, if not for the intervention of Caesar's former legate, Labienus. He scolded his own men for their lack of loyalty and proclaimed that the war would only end when Caesar's head was brought to him. Putting a stop to continued meetings between both sides, the timely effort of Labienus may have prevented a complete surrender of the Republican forces to Caesar, obviously forcing the matter to be settled in combat.
By spring of 48 BC, Antony managed to avoid the Republican fleet and finally make his crossing to Greece. Terrible winds pushed Antony and his 4 legions far north of his objective, and he was forced to land near Lissus, putting Pompey between the two much smaller armies of Caesar. Pompey ordered his legate, Quintus Caecilius Metellus Pius Scipio, to join him from Syria, and Caesar detached two legions under Domitius Calvinus to block this threat. Now Pompey raced to get to Antony while he was isolated, but Caesar didn't delay and followed closely behind. Pompey seems to have panicked at the thought of being caught between both armies, and maneuvered out from between both armies, while Caesar just continued northward to Antony, and the vital supply depot of Dyrrhachium. Pompey realized his mistake and tried to race to the depot, but this time, Caesar's men were faster. The two armies made camp on opposite sides of a small river called the Shimmihl Torrent, with Caesar on the north and Pompey on the south, and Dyrrhachium on Caesar's side of the river.
Understanding that supply and logistics was still the key, Caesar decided to use his great skill at siege warfare to hem Pompey in. Caesar's men built an impressive fortified wall of approximately 17 miles around Pompey's army, pinning it in against the sea. Pompey, rather than attack his still smaller opponent, responded by building a similar defensive work. While Pompey could still be re-supplied by sea, what he failed to realize was that Caesar controlled the flow of fresh water, and he immediately began to cut it off. Skirmishes were constant, and outside Dyrrhachium Caesar reports that the two sides fought 6 battles in a single day. Pompey simply couldn't break through and desperation was beginning to set in. By mid summer, though, Pompey had a fortunate stroke of luck. Two Gallic auxiliary were caught stealing the pay from legionaries, but managed to escape to Pompey. With these two men on his side, Pompey was able to discover the weakest point in Caesar's wall. A section to the south of the lines hadn't yet been completed and it was the only viable target for attack.
In early July, Pompey consolidated his army and struck with as many as 6 legions on the vulnerable position. Caesar's ninth legion, terrible overpowered, was forced to flee from the onslaught and Pompey established a new camp on the outside of the wall. Caesar attempted to reinforce the breach with 12 cohorts under Antony, and was initially successful in stemming the retreat. Caesar then drove back the Pompeians towards the sea, re-securing part of his wall in the process. 33 cohorts (3 legions) were sent against Pompey's new camp, but this is where things went terribly wrong. The attackers were outmanned nearly two to one and though initially successful, they simply couldn't sustain the advantage. Caesar's right wing began to buckle as it was flanked and threatened from the rear. As the wing collapsed, Caesar's army panicked and began to rout. Caesar personally tried to stem the retreat, but all was lost, and the only course of action was to attempt to save his army. Caesar really only lost 1,000 men in the battle, which was really a rather small affair considering the size of the armies, but the key was that Pompey could now claim a victory, and did so in earnest.
Pompey next made the most critical mistake of the entire war. Rather than continue to advance on Caesar's shaken lines, he decided to stand pat, seemingly feeling assured that Caesar was beaten and that the war was over. In reality, it very well could've been over if Pompey simply would've attacked Caesar throughout his lines. His army very likely would've fallen into a complete rout and been captured or killed en masse. Instead, Pompey seemed to lack the nerve to finish the job. Caesar himself said, that "Today the victory had been the enemy's had there been any one among them to gain it." Caesar gathered his army and moved away, hoping to lure Pompey away from his own source of supply. He followed initially, but petty squabbling within the Republican camp forced him to break off. Pompey and the Senators were more concerned over dividing up the spoils that were sure to come with victory than actually finishing the job. This respite granted Caesar enough time to invest and capture the town of Gomphi, where his army plundered and were fed. Re-energized, Caesar moved towards Pharsalus, where Pompey eventually moved to meet him.