The Abu Sayyaf - a separatist group still fighting
The military assault in the southern Philippines on followers of Muslim rebel leader Nur Misuari is the latest episode in a conflict that has been going on for about 30 years.
It was Mr Misuari's Moro National Liberation Front (MNLF) that began the Muslim separatist rebellion in this mainly Christian country in the 1970s.
He signed a peace agreement in 1976 - the Tripoli agreement - which failed to stick, and another 20 years later.
And, until he was arrested in neighbouring Malaysia on Saturday, he was behind the uprising on the island of Jolo in which more than 100 peole died.
All told, three decades of fighting in the southern Philippines has cost tens of thousands of lives and the killing goes on.
Peace agreement
After many attempts at a negotiated settlement, Mr Misuari and the government finally signed a peace agreement in 1996.
The agreement gave predominantly Muslim areas a degree of autonomy.
But Eric Gutierrez, of the independent Philippines Institute for Popular Democracy, said it was not enough for some MNLF members.
"It was basically a concession on the part of the MNLF, because they scaled down their demands from independence to autonomy," Mr Gutierrez told the BBC.
The more militant Moro Islamic Liberation Front (MILF), which had split from the MNLF, carried on fighting.
This year the government revived peace talks with the MILF and they concluded a ceasefire agreement.
Kidnap group
That left only the Abu Sayyaf still fighting. The Abu Sayyaf is another MNLF splinter group which has turned to kidnapping for ransom.
According to US intelligence reports, it probably also had links with several of the people who were involved in the 11 September attacks on New York and Washington.
In Washington last week, she told President George W Bush she was confident that the Philippines security forces had the willpower and the means to do that.
"Whether or not they are connected to al-Qaeda, they are terrorists," she said. "They terrorise two islands in the south-western corner of our country.
"But now it is not a lonely fight any more, because there is an international coalition against terrorism."
Return to arms
Mr Misuari, as governor of the Autonomous Region in Muslim Mindanao (ARMM), was a disappointment to both the government and the MNLF, so the MNLF removed him from its leadership.
Mr Misuari reacted by going back to war.
The MNLF is sticking to its peace agreement with the government and Mr Misuari commands the loyalty of only a small faction.
"After the trouble in Sulu that he started, and his finally leaving the island, Nur Misuari is now being viewed by the people of Sulu as an escapee - starting trouble and then abandoning his people," MNLF Secretary General Musliman Sema told the BBC.
Mr Misuari's return to rebellion is only an irritant to the government but it does illustrate the difficulty of bringing lasting peace to the south.