While Trump and many policy makers have focused on Trump, another old threat has not gone away: al Qaeda.
The group's leaders are still committed to attacking the West. AQAP (al Qaeda in the Arabian Peninsula) remains a deadly threat. Al Qaeda's leader, Ayman al-Zawahiri, says the priority is still to strike America "until it bleeds, militarily and financially."
So 15 years after al Qaeda's Sept. 11, 2001 attacks on the United States, Zawahiri continues to evade the Navy Seals who hunted down and killed his boss Osama bin Laden.
And in the Middle East, its offshoot Jabhat Fatah al-Sham is still a player in the Syrian war.
Beyond the immediate challenge of ISIS and al Qaeda, Donald Trump faces the diplomatic and policy dilemma of what to do about extremist groups' supporters in U.S. allies in the Gulf such as Saudi Arabia and Qatar.
Sunni Saudi Arabia and Shiite rival Iran have been at the heart of this problem by fueling proxy struggles that inflame sectarian struggles throughout the region. These conflicts only feed extremists like ISIS and al Qaeda.
America's ability to pull levers in Saudi Arabia, which has criminalized financial support for extremist groups while continuing to export a profoundly conservative version of Islam, has diminished as has its relationship with the kingdom.
Its reliance on the Saudis for oil is shrinking by the month as shale production rises in the U.S. In 2015, the nuclear deal with Shiite Iran enraged Sunni Saudi Arabia, which was already angered by Obama's unwillingness to back the Syrian opposition and what they saw as Bush's disastrous invasion of Iraq.
Meanwhile, hundreds U.S. soldiers are taking the fight to ISIS.
When Trump takes office, there will officially be around 500 Special Operations personnel in Syria. Their job is described as "support" and "training."
America's Kurdish allies claim U.S. Special Forces are already on the front lines. But a few hundred U.S. boots on the ground alone won't defeat the extremists.
The old order in the Middle East is collapsing as surely as the old borders of Iraq and Syria are disappearing. The new president needs to decide how much of America's capital he is willing to invest in forging a new regional balance of power.
Winning the peace in Iraq and Syria depends on a political settlement involving Russia and Iran and in the new American administration helping Sunnis believe in a future, in a government, that involves them.
Otherwise the sons of ISIS will rise from the rubble of Mosul and plague this new president — and many more.
Earlier in this series
Part 1: How China Could Pose the Biggest Challenge for Trump Yet
Part 2: Kim Jong Un's Nuclear Ambitions to Challenge Trump
Part 3: Nobody Will Test Trump Administration More Than Putin
Part 4: Can Trump Stop Syria War From Haunting U.S.?