About 10 years after Paul Muad'Dib gains the throne as Emperor of the Known Universe, the threat of the Jihad in his name still persists in Paul's prescient visions. Paul does everything to keep that Jihad from continuing, because this path can only lead to stagnation of the human race.
In "Dune Messiah" there continues that great Frank Herbert trademark of "plans within plans within plans." So with more patience this book can be very rewarding. The entire "original" Dune series is comparable to Tolkien's Lord of the Rings Trilogy, in scope and adventure.
In this book one of the many plots/conspiracies involved is that of reversing the events that led to Paul being emperor. This conspiracy is led by remnants of the displaced House Corrino, the Bene Gesserit who have lost control of their Kwisatz Haderach, the Spacing Guild, now utterly beholden to Paul, and the Bene Tleilax. They all scheme to kill Paul who has not produced an heir to the throne. In doing so a "ghola" of Duncan Idaho is grown by the Bene Tleilax and given as a gift to Paul. (A ghola is a clone, in this case of Duncan Idaho, one of Paul's closest confidants and mentors.) As time progresses it is found that this ghola named Hayt, actually has the memories of Idaho. However Hayt is sent to be the destruction of Paul Maud'Dib.
The reason Chani has not given Paul an heir is that Princess Irulan has been slipping contraceptives into her food. This causes Chani to think she is barren and she seeks out ancient Fremen fertility drugs. This cause her to become pregnant with twins.
At the time Hayt is to kill Paul he cannot do it, his conditioning is broke because of the memories of Duncan's love for Paul and House Atreides. Now an ally Hayt-Duncan, helps to stop the execution of Paul's newborn children.
In the meantime some Fremen Traitors use a Stone Burner to destroy a house that is faithful to the Maud'Dib, causing Paul to be blinded. This furthers the religious fervor behind Paul because with his prescience he can still "see." It is through this prescient vision that Paul thwarts the Tleilaxu face dancer's attempt at killing Paul's 2 children, Leto II and Ghanima. These children are as Paul's sister Alia, in that they are born fully aware of their prescient powers of being Kwisatz Haderach.
After this Paul goes by the way of Fremen tradition, where all the blind shall go to the desert as a sacrifice to Shai Hulud. Alia and Princess Irulan then raise the children to be heirs to the throne when they come of age.
Again this is simply the outer layer of the onion which is the Duneverse. Many plots within plots, plans with in plans and some great philosophical discussions hidden within a science-fiction novel. Next I move to "Children of Dune"...so be prepared for the ongoing adventures of Dune.