During his tenure as a minister in the Janata Party, he continued to be uncomfortable with certain elements of the broad-based Janata coalition, especially with the leaders of the erstwhile Hindu nationalist Bharatiya Jan Sangh in the Union Cabinet.
In a debate preceding a vote of confidence two years into the government's tenure in 1979, he vehemently spoke out against the practice of permitting members to retain connections to the Rashtriya Swayamsevak Sangh (RSS) while being in the ministry in the Janata Party.
The leaders of the Bharatiya Jan Sangh, among them Atal Bihari Vajpayee and Lal Krishna Advani, refused to give up their allegiance with the RSS, leading to a split within the Janata Party.
The issue of "dual membership" caused Morarji Desai to lose the vote of confidence, and his government was reduced to a minority in the Lok Sabha.
After the Janata Party started disintegrating in 1979, Charan Singh left it to form the Janata (Secular) Party and with support from the Congress Party, replaced Desai as Prime Minister.

In the seventh general elections held in 1980, the Janata (Secular) ministry failed to maintain a majority in the Lok Sabha, and Congress once again became the ruling party.
Fernandes retained his Parliamentary seat from Muzaffarpur in 1980, and sat in the opposition.
He contested for the Lok Sabha in 1984 from Bangalore North constituency against future Railway minister and Congress candidate C. K. Jaffer Sheriff, but lost the election by a margin of 40,000 votes.
He then decided to shift his base to Bihar in 1989, when an anti-Congress wave was sweeping the country in the wake of the Bofors scandal, and won Muzaffarpur in the 1989 and 1991 general elections, He later joined the Janata Dal, a party which was formed from the Janata Party at Bangalore in August 1988.
His second tenure as Minister of Railways in the V. P. Singh's government from 1989 to 1990, though short-lived, was quite eventful.
He was one of the driving forces behind the Konkan Railway project, the first major development in the history of rail transport in India since independence.

Fernandes broke away from the erstwhile Janata Dal and formed the Samata Party in 1994, which became a key ally of the Bharatiya Janata Party (BJP), a party which is the current form of the erstwhile Bharatiya Jana Sangh.
BJP formed a short-lived government in the 1996 general elections along with the Samata Party and other allies.
The government survived only for 13 days, since the BJP could not gather enough support from other parties to form a majority.
Fernandes later served in the opposition along with BJP during the two United Front governments (1996–1998) led by Janata Dal ministers H. D. Deve Gowda and Inder Kumar Gujral.
After the collapse of the United Front ministry led by Gujral, BJP and its allies won a slender majority in the 1998 general elections.
The government lasted only for 13 months, due to the non-co-operation of All India Anna Dravida Munnetra Kazhagam (AIADMK) leader Jayalalitha.

After the collapse of the second BJP-led coalition government, BJP and its allies formed a 24 party alliance called National Democratic Alliance (NDA), which became the first non-Congress coalition government in post-independence India to survive a full five-year term (1999–2004).
Later, Fernandes became the convenor of NDA.
On 27 July 1999, the Janata Dal again split into two factions, the Janata Dal (United) and the Janata Dal (Secular).
In 2003, Fernandes reunited with the Janata Dal (United), and also merged his Samata Party with it.
During his tenure as a minister in the Janata Party, he continued to be uncomfortable with certain elements of the broad-based Janata coalition, especially with the leaders of the erstwhile Hindu nationalist Bharatiya Jan Sangh in the Union Cabinet. In a debate preceding a vote of confidence two years into the government's tenure in 1979, he vehemently spoke out against the practice of permitting members to retain connections to the Rashtriya Swayamsevak Sangh (RSS) while being in the ministry in the Janata Party. The leaders of the Bharatiya Jan Sangh, among them Atal Bihari Vajpayee and Lal Krishna Advani, refused to give up their allegiance with the RSS, leading to a split within the Janata Party. The issue of "dual membership" caused Morarji Desai to lose the vote of confidence, and his government was reduced to a minority in the Lok Sabha. After the Janata Party started disintegrating in 1979, Charan Singh left it to form the Janata (Secular) Party and with support from the Congress Party, replaced Desai as Prime Minister.
In the seventh general elections held in 1980, the Janata (Secular) ministry failed to maintain a majority in the Lok Sabha, and Congress once again became the ruling party. Fernandes retained his Parliamentary seat from Muzaffarpur in 1980, and sat in the opposition. He contested for the Lok Sabha in 1984 from Bangalore North constituency against future Railway minister and Congress candidate C. K. Jaffer Sheriff, but lost the election by a margin of 40,000 votes. He then decided to shift his base to Bihar in 1989, when an anti-Congress wave was sweeping the country in the wake of the Bofors scandal, and won Muzaffarpur in the 1989 and 1991 general elections, He later joined the Janata Dal, a party which was formed from the Janata Party at Bangalore in August 1988. His second tenure as Minister of Railways in the V. P. Singh's government from 1989 to 1990, though short-lived, was quite eventful. He was one of the driving forces behind the Konkan Railway project, the first major development in the history of rail transport in India since independence.
Fernandes broke away from the erstwhile Janata Dal and formed the Samata Party in 1994, which became a key ally of the Bharatiya Janata Party (BJP), a party which is the current form of the erstwhile Bharatiya Jana Sangh. BJP formed a short-lived government in the 1996 general elections along with the Samata Party and other allies. The government survived only for 13 days, since the BJP could not gather enough support from other parties to form a majority. Fernandes later served in the opposition along with BJP during the two United Front governments (1996–1998) led by Janata Dal ministers H. D. Deve Gowda and Inder Kumar Gujral. After the collapse of the United Front ministry led by Gujral, BJP and its allies won a slender majority in the 1998 general elections. The government lasted only for 13 months, due to the non-co-operation of All India Anna Dravida Munnetra Kazhagam (AIADMK) leader Jayalalitha.
After the collapse of the second BJP-led coalition government, BJP and its allies formed a 24 party alliance called National Democratic Alliance (NDA), which became the first non-Congress coalition government in post-independence India to survive a full five-year term (1999–2004). Later, Fernandes became the convenor of NDA. On 27 July 1999, the Janata Dal again split into two factions, the Janata Dal (United) and the Janata Dal (Secular). In 2003, Fernandes reunited with the Janata Dal (United), and also merged his Samata Party with it.
George Fernandes