Youssef's "Daily Show"-style program has brought a new type of political satire to Egypt, and he gained plaudits for mercilessly skewering Morsi and his Islamist supporters for mixing religion and politics and for failing to implement much-needed reforms amid more than two years of turmoil following the ouster of autocrat Hosni Mubarak.
But the first show of the season faced a delicate balance as Youssef risked angering his mainly liberal fan base by criticizing the new military-backed government and army leader Gen. Abdel-Fattah el-Sissi, lionized in the media as a hero for removing the Brotherhood from power. Anything else would be seen as caving to pressure.
The 39-year-old surgeon-turned-satirist answered in Friday's episode of "El-Bernameg" Arabic for "The Program" by taking aim at the over-the-top, pro-military fervor sweeping Egyptians and jabs at el-Sissi with a series of jokes and skits.
The office of chief prosecutor Hesham Barakat said Monday it was investigating Youssef on a complaint that he disturbed the peace, harmed public interests, created chaos, sowed sedition and threatened security and peace. It also alleged that Youssef inappropriately ridiculed the Egyptian people, the armed forces as well as all "honorable national icons" without respect for traditions and customs.
Barakat's office received several complaints against Youssef after the program, but chose just one to be investigated in line with standing policy to focus on the best written and documented allegations.
The show comes against the backdrop of rising bitterness between the sides supporting and opposing Morsi, who has been detained and held at an undisclosed location since July 3. The ousted leader is scheduled to go on trial on Nov. 4 for allegedly inciting supporters to kill protesters outside his presidential palace in Cairo last December.
Many Egyptians are watching what happens to Youssef as a measure of whether the government installed by the military after Morsi's July 3 ouster is serious about shepherding the country toward democracy and freedom.
But activists said the fact that Barakat ordered an investigation into the complaint barely three days after the program was aired did not bode well for Youssef.
Heba Morayef, Human Rights Watch's Egypt director, said that while ordering an investigation into a complaint is routine, publicizing the decision is perceived as a serious step that could lead to an interrogation and a formal indictment.
"He (Barakat) is clearly responding to public pressure, or pressure from someone in particular," she said, without specifying who that might be.
About two dozen military supporters, who say the crackdown is a small price to pay if the country is to defeat what they view as Brotherhood-inspired terrorism, staged an anti-Youssef protest on Monday outside a Cairo courthouse, trampling on posters of the comedian and chanting slogans in favor of el-Sissi.
Youssef also faced legal action for his comedy during Morsi's year in office. The president's supporters sued him for insulting the presidency and Islam. He was questioned for hours by prosecutors, but was not charged with any crime.
Before returning to the air after a four-month absence, Youssef predicted in an article that he will continue to be pursued legally by his new critics "who allegedly love freedom dearly when it works in their favor."
In another example of how the political divisions are affecting everyday life, relatives and state media said an Egyptian kung fu gold medalist was suspended by the sport's national federation because he displayed an Islamist symbol showing support for Morsi during a tournament in Russia.
The newspaper Al-Ahram's online service posted a photo of Mohammed Youssef wearing a T-shirt emblazoned with a picture of an open palm with four yellow fingers the symbol commemorating a pro-Morsi protest camp violently cleared by security forces in August. In the photo, the athlete held his gold medal with his right hand while punching the air with a clenched left fist during the medal ceremony. He was sent home early from Russia and would be banned from a major tournament next month in Malaysia.
Islamic militants also have stepped up their campaign of violence since Morsi's ouster, mainly targeting Egyptian police and soldiers, especially in the volatile northern part of the Sinai Peninsula that borders Israel and the Gaza Strip.
The militants' campaign mostly has been confined to the troubled peninsula that is separated from the mainland by the Suez Canal, but attacks outside Sinai have grown more frequent in recent weeks.
On Monday, gunmen killed three policemen at a security checkpoint in Mansoura, a city north of Cairo, according to the Interior Ministry.