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After infecting a large number of the population with Omega symbols, Darkseid's homeworld, Apokolips began moving towards Earth, in an attempt to create a new Apokolips for Darkseid to rule. Granny Goodness, in a final attempt at recruiting Tess Mercer, revealed her lords plans to Tess, who refused to conform. Later, Granny Goodness, along with Desaad and Gordon Godfrey, had a possessed Oliver disable Watchtower's satellites so that Tess could not warn the League. However, thanks to a satellite activated by John Jones, Tess was able to see the oncoming planet. She attempted to contact Clark but was kidnapped by Lionel Luthor. After Tess escaped from Lionel, she shot him and left him for dead. Lionel crawled toward Lex, who had been comatose, and Darkseid offered to save Lex in exchange of Lionel's soul. Lionel agreed and was killed, but Lex was resurrected.
During Clark and Lois's wedding, the possessed Oliver attempted to subdue Clark using gold kryptonite, but Clark was able to free him from Darkseid's control, right as Apokolips came into Earth's orbit. Clark found Tess's car and heard the message she tried to leave him. He then searched for her in Luthor Mansion but instead met Lex once again, who promised that they shared a destiny together, but as enemies. Clark then went to the farm in order to find the Fortress's activation crystal, but was found by Darkseid, whom he defeated after mastering the ability of flight.
Oliver enters Watchtower and activates all of the computers. He searches for where Darkseid’s trio are hiding and once locating them with his satellites, reclaims his Green Arrow uniform. As Granny Goodness, Desaad and Gordon Godfrey declare their victory, Oliver arrives without his Omega symbol to the surprise of the others. Amidst their condemnation and rebuke, he tells them about his belief in Clark and that he will save them. Raising his bow, he fires three arrows simultaneously and vanquishes the trio.They disintegrate into clouds of smoke.
Lois snuck onto Air Force One in order to convince the Secretary of Defense not to launch a Nuke at Apokolips, which would result in the death of millions. After arguing that the Justice League would save them all, the Secretary decided to give them 5 minutes before the Nuke was fired.
With the Fortress reactivated, Jor-El gave Clark the Superman Suit in order for him to fulfill his destiny. Clark donned the new suit, saved the falling Air Force One and pushed Apokolips out of orbit, both saving Earth from destruction and from Darkseid's influence, and finally revealing himself to the world.
Images of aliens on Apokolips began surfacing, causing humanity to finally realize that they were not alone in the universe.
After revealing himself to the world, Superman became a global symbol for hope, and is now praised by millions due to his tireless efforts. Lois is now one of the top journalist in the country due to her report on the incident. Lex Luthor began his vendetta against Superman, after losing his memories, and now sees him as a threat to humanity. In order to prevent the possibility of invasion, Russia had launched defense platforms into orbit, prompting Lex to do the same.
- Lois and Clark reconcile their issues with being married and make it down the altar; however, the ceremony is interrupted by Oliver, who's revealed to have been corrupted to the darkness by Darkseid.
- When Granny Goodness talks to Tess about Darkseid's coming, she refers to Lucifer being a name for him in Earth legend. Just as beguiling and seducing as the Devil, Granny Goodness articulates false doctrine in order to win Tess over to her agenda. According to Biblical teachings, Lucifer - meaning "light-bearer" in Latin - by his own pride and rebellion, had been reduced to a "fallen" angel, subsequently becoming the Devil, now known as Satan. The paralleling morality elements of good versus evil also compare or liken Superman to Jesus Christ.
- While moving towards the Earth, Apokolips passes by and knocks into the rings of Saturn. In the comics, Saturn was home to a race of Martian clones, calling themselves Saturnians. Saturn's moon, Titan, is where Saturn Girl is from.
- As Tess tries to gain visual of outer space, Watchtower's computer says "Manhunter has put the new space station online per your request", which could possibly be referring to the future Watchtower that is seen orbiting space just like in the comics. John has also officially gained the Martian Manhunter nickname.
- Apokolips looks just like it does in the comics. It even can move, just like it could at certain times in the comics.
- Granny Goodness explains that Tess was born in darkness which is proven by being Lionel's heir, raised by Granny Goodness and abusive parents, and being Lex's sister.
- The "no tights, no flights rule" is officially broken when Clark flies away in the Superman suit.
- The finale episode contains various allusions to Superman feature films:
- Clark saving Air Force One combines elements of Superman: The Movie, in which Superman propped up the left wing of AF1, and Superman Returns, in which Superman saved a plane Lois was on. It also pays homage to the comics, where Superman's first public save was to catch the falling space plane where he first met Lois Lane. It's also the third time in the series he's rescued Lois, and in this instance the White House cabinet, from an aircraft.
- Superman throwing Apokolips back into space is similar to Superman Returns when Superman threw the mountain of kryptonite into space. Scene is also similar to Clark's actions in Season Ten's opener Lazarus when he runs in and leaps up to catch the Daily Planet globe.
- When Lionel and Tess talk at Lionel's lab, Lionel interrupts Tess by saying "wrong" which pays homage to Superman Returns where Lex shouts that when Lois was talking about Superman.
- Similarly, when Lois runs past a secret service agent to speak with the cabinet, she runs in the same way that Lois ran past the Eiffel Tower security guard to get to the elevator in Superman II.
- The Superman suit seen at the end of the episode is the costume worn by Brandon Routh in Superman Returns. However, the Smallville universe's major difference is that the suit has the emblem of the House of El on both the chest and the cape, while the one seen in Superman Returns only has the symbol on the chest.
- Lex being restored in his composite clone with pieces of the real Lex Luthor is a modified version of when Lex was in a younger clone of himself and posed as his own son in the comics.
- Lionel's deal with Darkseid parallels two different events in the comics:
- Lionel selling his soul to Darkseid in order to revitalize Lex within his composite clone parallels when Lex sold his soul rejuvenate himself within his younger clone from rapidly aging to Neron into something similiar to a modified version of his original age was.
- Lionel's heart being ripped out by Darkseid for Lex somewhat parallels Lex engineering his father's heart attack.
- Clark finally learns how to fly in this episode, after several previously failed attempts.
- Similarly, Lex loses his memories of his seven-year relationship with Clark, and so the story of Lex Luthor is aligned with comics where he does not know Clark until Lex becomes owner of the Daily Planet. However, recent publications have reflected the relationship between Clark and Lex and have made them the same age. In recent publications, specifically the "Origin of Lex Luthor" story, Lex moved to Smallville during his teens in order to clear his head and escape from his abusive father Lionel. While Clark, Lana and Pete all reached out to him, Lex chose not to show any form of friendship toward them, making himself an outsider.
- After the President's report on the radio about the "meteor" when Lois and Clark were at the Daily Planet, Lois says mentions the "Anti-Life Equation" which refers to what Darkseid is often searching for in the DC comics.
- Although that something may also mean she was the one who saved Clark from the only usage of gold kryptonite, which would theoretically permanently remove his powers.
- This is the only episode in which Darkseid speaks in his true form, however his voice actor is unknown.
- After Tess died and Lex is infected with the neurotoxin, the latter looks outside the window of LuthorCorp Plaza's office. After the bolt of lightning strikes, LUTHORCORP's signs changes to "LXCORP".
- One of Lex's erased memories depicts an unaired scene from Season Seven's Arctic in which Lex appears outside of the Fortress of Solitude.
- Clark's actions in the episode directly mirrors Superboy-Prime's of the comics. In Smallville, Clark became Superman after 10 years of trials which started during his first year of high school, where as in the comics Superboy-Prime completed his journey and became a superhero by the time he began high school. Clark pushing Apokolips away from Earth's orbit mirrors Superboy-Prime's act of pushing Thanagar into Rann in the comic books. Also, Clark pushing Apokolips away ended the JLA's war with Darkseid, where as Superboy-Prime began the Rann-Thanagar War.
- This episode shows that Lex covered up his scarred right hand with his trademark black glove similiar to ones showed in Hourglass, Scare, Void, Apocalypse, and Arctic.
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