The opponents of the Sangh started disturbances. There was stonethrowing in Nagpur and other places on 31st January. They attacked the house of Guru and pelted stones. Totally unperturbed, Guru kept on reciting Bhagavad – Gita with perfect equanimity and poise.

The Government arrested Guru under the baseless accusation of Gandhi's assassination. The Sangh was banned, and thousands of Swayamsevaks and workers were dumped behind the bars. Being alarmed by the growing strength of the Sangh, and due to the enormous public approbation Guru had been receiving all over the country, the Government cracked down on the Sangh in a bid to trample and finish it. There was in fact no connection whatsoever between the Sangh and the murder of Gandhiji. The Government had to withdraw the charges barely within a week. The courts of law released the Swayamsevaks and passed strictures against the Government action.

The Government released Guru also on 6 August with certain restrictions imposed on him. He entered into prolonged correspondence with the top leaders of the country. He appealed to the Government to lift the ban on the Sangh and to clear it of the charges, since they were all baseless. The restrictions on Guru too were eventually removed.

Guru went to Delhi. Thousands of citizens gave him a rousing welcome by showering flowers on him. Talks ensued. A suggestion was put forward for merger of the Sangh with Congress. Guru at once rejected it. Talks and correspondence failed. Preparations for a nation-wide movement to start the Sangh Shakhas in defiance of the ban order were set in motion overnight, with lightning speed. As expected, Guru was re-arrested. Sangh Shakhas was started in hamlets, villages, towns and cities all over the country again. More than a hundred thousand Swayamsevaks offered Satyagraha. They 
were promptly jailed. They were subjected to untold miseries and torture. People took out protest marches demandingimmediate removal of the ban. Many eminent personages came forward for mediation and began negotiation with the Government, The Swayamsevaks were denied even the minimum facilities that were normally made available to ordinary prisoners in the jails. As a result, their health condition began to deteriorate. Guru never bent before the Government. His cardinal faith was that "Ultimately Truth alone triumphs."

On 12 July 1949 the Government removed t the eighteen-month-old ban on the Sangh.

Guru advised the Swayamsevaks, "Forget the nightmarish episode of the ban. You should not harbor even the slightest bitterness in your minds about those responsible for causing us harm and injustice. After all they are our countrymen. Remember that both the tongue and the teeth always remain together. Once in a way by accident the teeth may bite the tongue; but on that account we do not knock them down. If one leg trips the other, are we to cut that leg? Those who have harmed us are very much our own people, not outsiders. Hence let us forget and forgive."