The wound that never healed
Fandral appears to have maintained contact with Leyara and her daughter, his granddaughter Astaria. The child was born after Valstann's death, and it's hard to say how much contact Fandral had with either of them. On the one hand, his devotion to and love for his son were so powerful it's hard to imagine he turned away from his son's only child and the mother of said child. On the other, having suffered so terrible and personal a loss (and remember, this was after thousands of years of presumed immortality), it's likely that he chose to isolate himself from them to some degree both to protect himself from any further loss and to protect them from his enemies, real or imagined.
During the passing of 10 centuries, Fandral's role in the defense of Kalimdor from the Silithid and his status as an powerful druid and close confidant to Malfurion helped keep him near the apex of druidic society. It's unknown what role, if any, Fandral played during the Third War and the battle for Mount Hyjal. Presumably he was one of Malfurion's allies in that battle, as almost all druids were. This seems most likely due to the fact that after the war and Malfurion's disappearance into the Emerald Dream, Fandral was the one to replace Shan'do Stormrage as Archdruid.
During this period, Staghelm and a faction of the druids decided to plant a new World Tree, in an attempt to regain the night elven immortality. This act, however, was not blessed by the dragon aspects the way the original tree Nordrassil was. While Teldrassil grew rapidly into a massive and majestic tree towering over the northern shores of Kalimdor, and the kaldorei settled into the branches, constructing their first new city in thousands of years amidst its boughs, all was not right with Fandral's new world tree. Darnassus grew rapidly into a major monumental city, but not only was the night elven immortality not regained, corruption soon began to spread through Teldrassil. Satyrs, grells, and other foul creatures made their homes in it.
Fandral soon proved an even more contentious and abrasive leader than would have been apparent from his past behavior. He clashed regularly with Tyrande Whisperwind, the chief priestess of Elune and leader of the Sentinels, the de facto military of the night elves. Believing in night elven superiority and the need for an aggressive military action against the invading orcs of Durotar, Fandral seemed almost to be regaining his old vigor and drive lost at Valstann's death. However, he also displayed a distressing sense of egotism and even outright racism towards the tauren druids taught by Hamuul Runetotem, one of Malfurion's students.
Over time, Fandral's strange actions began to worry others. Why was he collecting massive quantities of Morrowgrain? Why was he so determined to create a new World Tree against the wishes of those who had planted the first one? Why was he so interested in the Idol of Remulos, an artifact given to the druid Broll Bearmantle by Remulos, son of Cenarius?
Everything came to a head during a ritual that supposedly would have helped cleanse Teldrassil of its corruption. It was discovered that rather than purifying the tree, Fandral was in fact responsible for its being corrupted in the first place. Fandral was no longer in control of his own actions. Rather, he was an unwitting pawn of the father of all satyrs, Xavius, who had been transformed into a tree by Malfurion during the War of the Ancients.
Xavius, in his guise as the Nightmare Lord, servant of the entities behind the Emerald Nightmare's encroachment on the dream, had appeared to Fandral in the form of his son Valstann. Fandral had never been able to reconcile his failure to save his son, and the visitations played on his guilt and rage, eventually driving him to a kind of madness that blinded him to the truth. He chose to believe that Valstann had returned and that all of his actions at "Valstann's" urging were for the greater good. Using Morrowgrain to keep Malfurion trapped in the dream, grafting a branch of Xavius' nightmare form onto the young Teldrassil, anything and everything Fandral did he did believing it would fully restore his son to life
During the events of the novel Stormrage (where all of this played out), Fandral's delusion ended up being forcibly shattered, as the image of Valstann was destroyed and he fell into a state of near-catatonia. Malfurion managed to defeat Xavius, but Fandral was left a broken husk, forced to endure the loss of his beloved son for a second time. And thus he remained, one of the most powerful druids on the face of Azeroth, abandoned by his order, the discarded tool of a devious liar.
(Spoilers for Patch 4.2 incoming.)
Fandral's story might have ended there if not for the Cataclysm. While Fandral himself lay shattered in Moonglade, his daughter-in-law Leyara and granddaughter Astaria were living in the ancestral night elf territory of Ashenvale. While the druids of Moonglade eventually concluded that they lacked the ability to help so powerful and damaged a mind as Fandral's, the orcish Horde attacked Ashenvale, burned Astranaar, and killed Valstann Staghelm's daughter, the last living link Fandral had to his son.
The Twilight's Hammer, working ultimately for the selfsame Old Gods Fandral had once balked in Silithus, sought out the shattered Archdruid with the aid of a traitorous green dragon named Alysra. Somehow, they managed to restore Fandral to a state somewhat resembling sanity.
In that state, he looked upon the destruction of his granddaughter and saw his son's wife and her grief over the loss of her child, so similar to his own. Viewing her as a kindred spirit and the only remaining piece of his lost son, Fandral visited Leyara and told her of his vision of a new order of druids who would not merely sit back and allow the Horde to murder their children and steal their land. Leyara became the first of Fandral's Druids of the Flame, a twisted order serving Ragnaros the Firelord and through him, the Old Gods.
In his 9,000 years of life, Fandral has gone from being one of the greatest enemies the Old Gods have ever had (to the point that the Qiraji minions of C'thun even named him as such) to a servant of one of their Elemental Lords.
In time, Fandral will confront his former Shan'do directly, as well as the Earthen Ring's greatest champion, Go'el son of Durotan. As Majordomo of the Firelord Ragnaros, Fandral is one of the greatest champions of those who wish to see the whole world burn ... the world that killed his son and his granddaughter, while others stood back and mouthed platitudes.