Anakin must face the Son and the pull of the Dark Side. The Son already knows how to manipulate and twist him. Once Anakin sees his future, will he be able to leave Mortis and the Son? The most recent episode of Star Wars: The Clone Wars, “Ghosts of Mortis,” makes Anakin face his true path.
At the end of the previous episode, the Father warned Anakin that he must get back to his ship as fast as possible. The Son needs it to leave Mortis, and they can't allow that to happen. The ship took a lot of damage last time they landed though. Ahsoka tries to repair the ship (she should wear mechanic's goggles more often, they suit her) while Anakin and Obi-Wan sit around and talk. Well done, Ahsoka. Since the repairs will take a while, Anakin decides to speak to the Father. He is not sure that he is doing the right thing by leaving; the Son is strong and maybe the Father can't contain him. He doesn't want to be haunted by the wrong decision.
The Father is heartbroken over his daughter. He has just left the Dagger of Mortis in her cold hands when Anakin arrives. He is angry and surprised that the Jedi haven't left yet. It's too dangerous to have that open escape route for his son. He tells Anakin that he must destroy his son. It is the only way to assure that the Dark side will not overrun the universe. Anakin wants to help, but the Father tells him the choice is no longer his. He advises the Jedi to ask for the answers he needs.
Anakin follows a nondescript path on the Force-strong planet seeking answers. The spirit of Qui-Gon Jinn appears to him. He tells his former padawan that he believes he is the Chosen One that will bring balance to the Force. He also advises Anakin that he must look deeper to find a way to deal with the Son. He sends the conflicted Anakin to a deep well of the Dark side.
Back at the ship, Obi-Wan tells Ahsoka to stop repairs. He is going to search for Anakin. As Obi-Wan steps off the ship, he sees the Father. The Father tells Obi-Wan that he has not ordered Anakin to do anything; he just sent him off to find answers. And those answers happen to be in the well of the Dark side. That does not make Obi-Wan happy. The Father warns him that he shouldn't interfere, but Obi-Wan ignores him and heads after his friend.
The deep well looks a lot like the volcano planet of Mustafar. Lava runs down the side of the walls in rivulets, and ashes float in the air. Anakin spirals down and lands at the bottom of the well; he is immediately confronted by the smooth-talking Son. Anakin is unforgiving at first. He draws his lightsaber, but the Son reminds him that it is useless. He distracts Anakin with visions of his future. “Know what you will become,” he tells Anakin. You see flashes of the Emperor, Padmé crying out in pain and shock, Younglings being killed, and finally – the helmet of Darth Vader. The Son uses these visions to twist Anakin to join his side. They will destroy the Emperor, stop the war, and bring peace to the galaxy. They will change Anakin's destiny.
Obi-Wan arrives too late to talk sense into Anakin. He confronts Anakin, but he is beyond help. He tosses Obi-Wan's speeder into the lava. He tells his former Master that he must stop the war, and the Jedi are only in the way. Anakin leaves with the Son. Obi-Wan calls back to the ship and tells Ahsoka that Anakin is lost. He tells Ahsoka to disable the ship entirely even though she just fixed it. The Son and Anakin cannot leave. Ahsoka takes a key part of the ship and as soon as Anakin arrives, she steals his speeder.
She gets away and helps Obi-Wan with his long climb out of the Dark side well. They head to the Father's monastery. At the ship, the Son realizes that they are unable to leave. He decides to visit his Father and force him to somehow let them off the planet. He leaves Anakin behind and as it turns out, the Father was right there all along. Anakin tells him that he knows his future, and he is joining with the Son so that he can prevent the terrible things he will do and the pain he will cause. The Father knows that there cannot be balance if Anakin has seen his path. His Son has broken the laws of time. The Father touches Anakin's forehead and erases the visions from his memory.
The act knocks him unconscious, and the Father took him to his monastery. Anakin awakens just as Obi-Wan and Ahsoka arrive. They decide that the Son must be destroyed, and the Father more or less tells Anakin that he has to be the one to do it. The Son arrives to the monastery. The Father begs him to restrain himself and to stay on Mortis, but he refuses. The Jedi all try to attack, but the Son bats them away as if they were flies. The Father notices the Dagger of Mortis hanging from his son's belt though. The Son visited his sister's tomb and took it. The Father takes it and turns the dagger on himself. As he kills himself, the Son suddenly realizes that he does not want his father to die. He begs his father not to die, and while he is distracted, Anakin kills him. The Son is dead, and the Father dies heartbroken. Before the Father dies, he tells Anakin that he has brought balance to Mortis. He must stay on this path and do the same for the galaxy.
The Father disappears as he dies, and Mortis starts to crumble around them. A bright white light (like the one that brought to Mortis) consumes the Jedi. They awake on their ship to Rex calling them. Rex tells them they were off the radar for a moment. Only a moment. That's going to be a fun debriefing back at the temple.
Trivia & Notes
According the StarWars.com episode guide, the fact that the Father was the only one of the family to disappear like Yoda and Obi-Wan was intentional.
Anakin's internal journey on Mortis was meant to be very much like Luke's journey in the cave on Dagobah, another place in the universe that was particularly strong in The Force.