This post contains major spoilers for the ending of The Umbrella Academy Season Two.
The Hargreeves siblings spent Season Two of The Umbrella Academy much as they did Season One: hurtling towards the apocalypse. In the end of the new season, they're able to avert the end of days. But this time, that's not the the biggest fight they're facing. After Ben sacrifices himself in order to talk Vanya down from using her powers to blow up Dallas's FBI building, which the government would have taken for a Russian attack and responded with an attack that sparked a nuclear war, the Hargreeves are in the clear apocalypse-wise, they still have to face off against one major foe: The Commission.
What's going on with Harlan?
After crash-landing in Dallas, all of the Hargreeves kids build new lives for themselves. Vanya winds up as a nanny for a kid named Harlan, who has autism, and she embarks upon a romance with Harlan's mom, Sissy. At one point earlier in the season, Vanya saves Harlan from drowning in a local pond by giving him mouth to mouth resuscitation. While bringing the kid back to life, Vanya inadvertently passes some element of her powers to him.
Everyone's got their own side stories going on, and for most of the season these take a backseat to the apocalypse. But after Vanya is safely secured from ending the world, things with Harlan and Sissy really start popping off. Harlan's father, Carl, decides to follow through on his longtime-threat and have his son institutionalized, so Sissy breaks out her shotgun and tries to shoot her husband. The gun accidentally discharges in the ensuing scuffle, and is heading straight for little Harlan—until he uses Vanya's energy-controlling superpowers to turn the bullet around in its tracks. It strikes Carl, killing him. Unable to control his new powers, he produces an energy vortex that threatens to spin out of control, so Vanya and her siblings head to the rescue.
How does the Commission come into it?
The Handler has been gunning for the Hargreeves kids since Season One, and their habit of screwing around with the timeline that the Commission is charged with keeping in order hasn't endeared them to her since. With her adoptive daughter Lila in tow, she follows the Umbrella Academy to Sissy's farm, determined to kill the Hargreeves siblings and kidnap the intriguingly powerful Harlan. Lila, having learned that Five was the assassin who murdered her birth parents when she was a child, is more than down to slaughter the Umbrella Academy, despite her recent fling with Diego.
The Handler also has a pretty convenient cover story that makes killing the Hargreeveses look like official Commission business. She owes her rapid climb up the corporate ladder to the fact that she struck a deal with Five, promising to help his family return to 2019 in exchange for him killing the Commission's board of directors. (After Five slaughters the board, the Handler gives him a 90 minute deadline to assemble his siblings and time warp out of Dallas—a deadline the family completely fails to meet.) So, in the guise of seeking vengeance for the board of directors, the Handler sics all of the Commission's assassins on the members of the Umbrella Academy.
Vanya's able to lay waste to them all with a single energy blast. But hundreds of expertly-trained assassins are nothing compared to the weapon the Handler has in store.
Wait, who has powers now?
That's right, the Handler's adoptive daughter Lila is one of the 43 super-powered kids born on October 1, 1989. And she has a particularly useful gift—she's able to channel the powers of others. She packs an energy blast that lays Vanya flat, is strong enough to take down Luther, and can teleport when she's fighting with Five.
But Five reveals to Lila that it was actually the Handler who ordered her parents killed, and Diego tries to persuade Lila that her mother only wants to use her to gain power for herself. Right when it looks like Lila was about to abandon the Handler and slap an umbrella patch on her arm, the Handler shoots all of the Hargeeveses dead, before turning her machine gun on Lila.
The last remaining Swede, who's pieced together that the Handler duped him and his now-dead brothers into serving as her own personal assassins, had followed the Hargreeveses to the farm. But he's no longer just trying to kill the Umbrella Academy—instead, he shoots The Handler to death, before turning his gun on a dying Five.
Badly wounded, Five remembers Reginald Hargreeves' advice about using his powers. Things always seem to go wrong when Five tries to travel through time, and Reginald told him to "start small—seconds, not decades." With that in mind, Five is able to wind back the clock to seconds before his siblings are shot, and takes the Handler's gun from her. The Swede still shows up, kills the Handler and declares a truce with Five. Lila grabs a briefcase and disappears for eras unknown.
Vanya is seemingly able to transfer Harlan's powers back to herself, and Herb, the new head of the commission, lets the Umbrella Academy use a briefcase to travel back to 2019. Allison leaves her husband Ray in 1963, and judging by his ability to float a toy, Harlan still has a little bit of Vanya's gift left in him. The Dallas storyline is resolved—but the last scene of the episode opens the door to Season Three.
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