This is a very basic overview and goes into almost no detail. It is just a rough outline of some complex situations.

US has to pressure India to give up the Muslim dominant regions of Jammu, the Kashmir Valley, and Ladakh to Pakistan. With those areas under Pakistani control, Pakistan will no longer need to 'secretly' support the jihadists in their country and the jihadists fighting India in Kashmir will no longer need to do that.
With that solved the US will be more effective in pressuring Pakistan to crack down on their Islamist extremists since they no longer need them for the jihad in Kashmir. Pakistan also has to throw its support behind the Islamic Republic of Afghanistan. With their support base in Pakistan gone the Taliban will become less effective and dwindle off.
With that dealt with Afghanistan will be able to handle the security situation in their country. Afghanistan should not try and have a strong central government and instead opt for a federal system with a central government that controls the things that affect all the Afghan states. This should reduce the tension between different groups in Afghanistan.
The US has to seriously pressure Israel to grant full independence to the West Bank and Gaza Strip. Even to the point where the US removes all financial/military support if it comes down to that. With an independent Palestine the other Arab states should be able to accept Israel more.
The Arab states that receive military support from the US need to be pressured by the US to become more free and open societies. With those governments becoming more open and free, the radicals will have less to complain about.
The economic power of all the Arab states also has to boosted. More jobs means less people becoming radicalized.
This will also make it easier for Iraq to fix its security situation because prosperity reduces radicalization and there will therefore be less people drawn to the groups that are spreading terror across Iraq.
With the rest of the Middle East and South Asia getting better, the US will need to ignore Iran. Iran does not pose an existential threat to the US. Iran is also very far away and cannot harm the US. Once this occurs the moderates in Iran should be more able to spark internal change in Iran. Once the change starts the US should be willing to lend a helping hand to the moderates in further developing the changes.

Not saying it will be done, but that's what should be done.

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"We consider this our duty - to defend humanity against the scourge of intolerance, violence, and fanaticism." -Ahmed Shah Massoud
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