How does a Prayer really work and the science behind it?
In the Name of Allah the Most Gracious and Ever Merciful
“The principle of prayer is that there is a mutually attractive relationship between a pious servant and his Lord. To begin with, the mercy (Rahmaniyyat) of God Almighty draws a servant to itself. Then through his sincerity the servant approaches close to God Almighty and in prayer that relationship, when it arrives at a certain stage, manifests its wonderful qualities. When a servant being confronted with a great difficulty leans towards God Almighty with perfect certainty, perfect hope, perfect love, perfect fidelity and perfect resolve, and becoming extremely alert and tearing aside the veils of heedlessness advances far into the fields of the discarding of self, he beholds in front of him the court of the Divine and that He has no associate. Then his soul prostrates itself at that threshold and the power of attraction that is invested in him draws the bounty of God Almighty towards itself. Then God, the Glorious, addresses Himself towards fulfilling the purpose of the supplication and casts the effect of prayer on all those preliminary means which give rise to the means that are necessary for the achievement of the purpose of the prayer.
For instance, if the prayer is for rain then on its acceptance the natural means that are needed for rain are created by the effect of the prayer. If the prayer is for famine the All-Powerful One creates the contrary means. It has been proved to the satisfaction of those who have frequent experience of visions that in the prayer of a perfect person a power of fashioning is created. That is to say, by the command of God the prayer exercises control in the lower and higher world and turns the elements and heavenly bodies and the hearts of people to the direction that is desired. There are many instances of this in the holy Books of God Almighty.
The Effect of Prayer is Greater than the Effect of Fire
Some types of miracles are in reality the acceptance of prayer. The source of thousands of miracles that were manifested by the Prophets and the wonders that have been exhibited throughout by the saints was prayer, and it is through the effect of prayer that extraordinary events display the power of the All-Powerful.”
Excerpted from The Essence of Islam Volume II (pp 192–194)