When Caesar crossed the Rubicon the Senate finally realized that they had made a terrible mistake. The mistake wasn't in letting the situation get that far, but in that they believed the Roman and Italian people would rally to defend the Republican system. What they failed to understand was that the people had little trust in the Senate and that Caesar had won them over through his popular agenda while in political office. Caesar's great propaganda campaign, his books "Bellum Gallicum (the Gallic Wars)" endeared the people even more to their almost mythical hero, and the Senate's cause in Italy was lost. Unable to levy armies, or develop a meaningful resistance, the Senate, and Pompey had little choice but to take their business out of Rome and into Greece. It was here, and further east, where Pompey held considerable sway, where the Senate hoped to raise armies and defeat Caesar.
This too, however, worked in Caesar's favor. Without the fear of bloodshed and damage to their homes in Italy, the people had little reason to support the Senate. Caesar marched throughout northern Italy accepting the capitulation of cities and garnering support with little difficulty. Pompey and the Republicans, meanwhile fled to Brundisium in the heel of Italy, where they hoped to secure the bulk of the transport vessels available in the region. The bulk of Pompey's forces were removed across the Adriatic to Dyrrhachium, along with the bulk of the Senate, but by early March of 49 BC, he still had nearly 2 full legions with him in Brundisium. Caesar approached quickly with 6 legions in an attempt to put an end to the resistance then and there. Attempting to box Pompey in, Caesar tried to negotiate peace, but Pompey delayed just long enough to make good his escape. Despite Caesar's attempts to block the harbor, the Republicans controlled the navy and Pompey escaped with his forces intact.
Caesar now faced an important choice. Without transports, he would have to face a difficult crossing in order to pursue Pompey, and Pompey's large army of 7 legions waited without their commander in Spain. He also needed to go to Rome to settle a situation that was certainly bordering on riotous. Though Caesar so far had shown clemency to his opponents, people in Rome weren't sure if the new conqueror would be like Sulla and Marius. To complicate matters further, Caesar's Legate Titus Labienus, who was left in command of Cisalpine Gaul, decided to switch sides and support Pompey. Caesar decided the best course of action was to settle matters in Rome, then move north to deal with Labienus, and then west to confront Pompey's army in Spain. His legate Curio was sent to Sicily with 3 legions where the ultra-conservative Cato was governor, to not only stamp out resistance, but to secure its valuable grain supplies. Cato fled to Africa, angry at Pompey for abandoning Rome, Italy and Sicily without a fight and certainly because of the hated Caesar's success. Caesar sent another legate, Valerius, with 1 legion to secure Sardinia.
With the immediate neighboring provinces handled, Caesar moved on towards Rome, but first held a meeting with Cicero in Formiae. Caesar attempted to have the great orator join him in Rome to help legitimize his new government. Despite the consternation of Cicero against his 'optimate' friends, he still maintained more common ground with them and refused without certain conditions. Caesar, against Cicero's proposed solutions agreed that it would be best to part ways, but certainly lamented the inability to secure Cicero's support. Continuing towards Rome, Caesar arrived at the end of March, 49 BC, for the first time in 9 years. This visit however was short-lived. Aside from securing the treasury for his own war efforts, an incredible total of 15,000 bars of gold, 30,000 bars of silver and 30 million sesterces which the Republicans had neglected to secure in their haste to leave, Caesar spent less than a week in the eternal city. In early April, Caesar prepared to march for Spain saying, "I go to meet an army without a leader, and I shall return to meet a leader without an army"