Who runs the government at the national level under the parliamentary system?

The Prime Minister and Council of Ministers

The correct answer is Option 2  - The Prime Minister and Council of Ministers

Under the parliamentary system, the government at the national level is run by the Prime Minister and the Council of Ministers.

Important Articles: COM, Prime Minister, and Attorney General

Article 74: Council of Ministers to aid and advise President
Article 75: Other Provisions as to Ministers (appointment of the Prime Minister)
Article 76: Attorney-General for India
Article 77: Conduct of business of the Government of India
Article 78: Duties of Prime Minister with respect to the furnishing of information to the President, etc.