Following the Munich crisis, Czechoslovakia was taken over by Nazi Germany quite easily and without a fight. The Munich agreement saw the country basically abandoned by its western allies in an attempt to appease Hitler, and much of the mountainous border was ceded to Germany. This left the country in an indefensible state, as it was in these regions where Czechoslovakia had started with the construction of a series of fortifications a few years prior. It needs to be said that even if Sudetenland had not been acquired by Germany a Czechoslovak defense would be difficult at best, as these defensive works were nowhere near ready by the time of Munich.
What followed is a short lived period known as the Second Republic, which lasted from the first of October 1938, the day after the Munich agreement came into effect, until halfway through March 1939, when German troops crossed the new border into Czechoslovakia. Or, to be precise, Czecho-Slovakia, as the country was called during this short and turbulent time.
The events of Munich and the subsequent First Vienna Award (which saw parts of Slovakia ceded to Hungary) had caused a major internal crisis in the country, with president Edvard Beneš abdicating, replaced by Emil Hácha; the partially fascist Slovak People's Party successfuly pushing through for autonomy of Slovakia within the state (hence the hyphen), a move welcomed by Germany; and a sharp turn towards authoritarian politics and attempts at appeasing Hitler and preventing further trouble.
Thus by late 1938 the stage was set for Germany to take over the rest of the country with ease. Czechoslovakia was facing severe internal issues, had lost about a third of its land and significant parts of its industry, and was under major pressure from Germany in matters both domestic and foreign. Already just two weeks after the Munich agreement did Hitler assign to his staff the task of coming up with a plan to deal with what remained of Czechoslovakia as soon as possible. Last but not least, unrest and even armed clashes between Czechs and Germans were common in the border regions.
On March 14, 1939, following a meeting between Jozef Tiso, the leader of the Slovak People's Party, and German leadership in Berlin, Slovakia declared independence. On the same day, Hácha left for Berlin to meet with Hitler. In the evening, small numbers of German troops crossed the border, a day before the full fledged occupation. Most notably in Frýdek-Místek, where an isolated act of Czechoslovak military resistance saw an army company led by captain Karel Pavlík clash with a force of Germans sent to secure the local barracks. Which they did the following day after a ceasefire, as neither side attempted nor wanted to escalate the skirmish.
Shortly after midnight, Hácha met with Hitler and was informed that in a few hours, the German army would cross into Bohemia, Moravia and Silesia. He was warned against resisting the invasion, with the German side threatening reprisals and a much harsher treatment of the country, supposedly including the bombing of Prague, afterwards. Presumably succumbing to the pressure and stress, Hácha had suffered a heart attack in between the talks and required medical assistance before continuing. Ultimately, the Czechoslovak side accepted the German demands.
Three hours after midnight, the Czech army was ordered not to oppose the invaders. At 4.30 in the morning, local radio started to announce the immediate arrival of German troops. Prague was occupied by noon, and Hitler himself arrived in the capital in the evening. The next day, on March 16, at Prague Castle, Hitler proclaimed the establishment of the Protectorate of Bohemia and Moravia. The Czech rump state was now fully in the hands of Nazi Germany.