When Crowley admits that he cannot get Sam's soul back, Castiel burns Crowley's human remains. At the end of the episode Castiel explains to Sam and Dean that the celestial war is not going well for him and he would rather be on Earth with them, but leaves anyway to continue fighting, but promises to take care of Crowley's captured monsters first.
After acquiring the holy weapons from Balthazar in "The French Mistake",  Castiel suggests that he now has a military advantage in the war. Unfortunately, this advantage seems limited; he orders Balthazar in "My Heart Will Go On"  to save the Titanic , spawning 50, new souls to empower his side.
However, Fate works to undo the impossible births and begins killing them. Once the brothers encounter the string of odd deaths Fate takes this opportunity to eliminate them due to their part of undoing the destined Apocalypse.
III. THE PREPARATION FOR THE PUBLIC MINISTRY
This forces Castiel to concede the loss and re-sink the Titanic. In "Frontierland", Sam and Dean call for Castiel to send them back in time as they have learned that the ashes of a Phoenix can kill Eve and that Samuel Colt killed one in the past with The Colt. Rachel, Castiel's lieutenant comes instead and berates the boys for only calling for him when they need something of him, but Castiel arrives himself and sends Rachel away.
Castiel is able to send Dean and Sam back in time, but warns them that he has to retrieve them in 24 hours or they'll be stuck in the past forever and tells Bobby to pray for him when the time comes. While waiting, Rachel approaches him about his plans and attacks him.
Castiel kills her, but is left weakened by a stab wound she managed to inflict on him first. Castiel manages to teleport to Bobby's and draws a sigil to hide himself from the other angels before passing out.
What Does the Bible Say About Angels?
He wakes in time to retrieve the Winchesters, but his weakened state prevents this so he is forced to draw power from Bobby's soul. While Dean killed the Phoenix, Castiel brought them back before they could gather the ashes so it all appears for nothing and he lacks the power to send them back. Luckily, Samuel Colt collected the ashes and sent a package with them to be delivered to Bobby's after the boys return.
In "Mommy Dearest", it is discovered that there is a possibility Crowley may have faked his death and might still be alive; suggesting that perhaps Castiel had burned the wrong bones by mistake. Eve reveals this to Sam and Dean when they try to hunt her down. During the hunt, Eve is able to suppress Castiel's powers as she is older than him. After Dean kills Eve, Castiel's powers return and he kills all of her monsters with a blast of white light before transporting the group to the home of the uncle of two young boys who were turned into monsters. There, they find them dead, having been killed by demons, and Castiel promises to look into Crowley's possible survival to find out for sure if he's dead or not.
In "The Man Who Would Be King", it is revealed that Castiel was the one who partially raised Sam from Hell, though due to the complication of the cage it was impossible to retrieve his soul, and that he has made a deal with Crowley in a desperate attempt to win the war. Sam and Dean also learn of his partnership with Crowley when he slips up and reveals he is spying on them.
In "Let it Bleed", Castiel is enraged to learn that Lisa and Ben Braeden have been kidnapped by Crowley and tries to get him to reveal where they are to no avail. Castiel saves Dean from a demon and tries and fails to convince him to back off.
Later, after Lisa is mortally wounded by a demon possessing her in an attempt to force Dean not to exorcise her, Castiel arrives at the hospital and without being asked, heals her wounds and at Dean's request, erases all of her and her son Ben's memories of Dean. He does this as a final act of friendship towards Dean though both admit it doesn't change the fact that they are now enemies. Castiel also spends the episode one step ahead of Bobby investigating H.
Lovecraft's opening of Purgatory in an attempt to find a way to open it himself.
He demonstrates his new power by killing Raphael with a simple snap of his fingers. While talking to Dean, who unsuccessfully begs him to give up the power, Sam sneaks up behind them and attempts to kill him with an angelic blade by stabbing Castiel in the back, but it has no effect. Castiel removes the blade, explains that he is no longer an angel, declaring himself their new God.
Castiel (Supernatural) - Wikipedia
He then glances at the three hunters before delivering an ultimatum: to profess their own loyalty and love unto him, or be destroyed. In "Meet the New Boss", Castiel begins exacting his new supremacy over the planet, working miracles and punishing religious hypocrites alike. However, when Castiel's vessel begins to become damaged and he begins to lose control of his power, Death reveals that he also absorbed creatures known as Leviathans from Purgatory.
The Leviathans will destroy him if they are not released. Castiel seeks out the Winchesters' help, and reopens the portal with Death's assistance. Although the souls are returned, the Leviathans evade reentering Purgatory and take control of Castiel's vessel.
In "Hello, Cruel World", the vessel begins to quickly break down. The Leviathans are forced to leave, dispersing into the local water supply nearby and leaving behind only Castiel's trench coat. After the Leviathans left him, he made his way out of the river, naked, and ran into his future wife Daphne.
However, the experience renders Castiel amnesic, but with his angelic powers intact. Going by the name "Emanuel", Castiel used his powers to heal people, though he didn't know where that ability and his power to see demon's true faces came from. After Sam is committed to a mental hospital as a result of the hallucinations of Lucifer he is suffering due to Castiel breaking his "mental wall", Dean searches for "Emanuel" and kills a demon that is holding his wife hostage. Castiel agrees to help Dean who doesn't tell him who he really is, but mentions what "Cas" had done to Sam.
The two are joined by Meg, but upon reaching the hospital, find demons surrounding the entrance. As Castiel is the only one who can take them all down, Dean is forced to tell him the truth about who he really is and insists he has the power to kill the demons. Castiel manages to summon his power to kill demons and kills all of them, but doing so restores his memories. Castiel shows remorse for his previous actions and initially wants to leave, but Dean is able to convince him to help by giving him back his trench coat.
Castiel finds Sam in time to save him from a demon torturing him to death with electro-shock therapy and tries to restore his mental wall, but can't as it's completely gone. Feeling sorry for what he had done, Castiel transfers the problem to himself and is haunted by visions of Lucifer like Sam was. Castiel is committed to the mental hospital, but is safe from the demons as only Meg knows he's alive and she takes a job at the hospital, presumably to look after him.
In "Reading is Fundamental", Castiel is awakened when the Word of God — a tablet with information inscribed by an angel as dictated by God — is found by Sam and Dean. Although his torment has driven him insane, he explains that taking on Sam's pain has helped relieve some of his past burdens. He then explains what the Word of God is, but is unable to read it. Two angels from his former garrison arrive in pursuit of Kevin , a prophet who was awakened by the Word of God and drawn to it. The angel Hester tries to kill Castiel out of anger for his past actions, but she is instead killed by Meg.
The other angel offers Castiel the chance to return to Heaven with him, but Castiel declines, explaining that he feels he no longer belongs there. The other angel then leaves, taking Kevin away to safety. Castiel comments to the Winchesters that he finds it amazing that he does not know what he is going to do next, and teleports away after giving them his blood.
In "Survival of the Fittest", after finding his garrison wiped out, Castiel has Meg take him to the Winchesters where he explains what he has discovered. Crowley arrives and is furious to see him, but Castiel no longer has a wish to fight and when Crowley realizes he's insane, he decides to put off his feud with Castiel for a time when he's sane again. Crowley, after giving them his blood, disappears but tells them Castiel can help them kill Dick.
Castiel refuses to help as he doesn't want to fight and after he disappears to retrieve a board game, Meg explains that since Castiel had the Leviathans within him, he is able to tell them apart even in their human forms and can pick out the real Dick Roman. Castiel watches as Sam and Dean burn Bobby's flask and put him at rest and later takes Dean to where he has stored the Impala and agrees to help.
Dick throws Castiel across the room when he tries to attack, but after Dean fails to kill Dick, Castiel holds his head in place from behind allowing Dean to stab Dick through the neck with the weapon, killing him. As a result of this, Castiel and Dean are sucked into Purgatory with Dick's soul and after letting Dean know this and that they are more likely to die than get out, Castiel disappears, leaving Dean alone.
He later tells Sam that things got hairy near the end and that Castiel didn't make it, that he "let go". While Dean doesn't elaborate, he is clearly affected by this.
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In a flashback scene, Dean is shown looking for Castiel in Purgatory, interrogating a vampire for his location. As a result, he meets Benny and only agrees to Benny's deal to get out if they find Castiel first and help him escape too.