With Number Five - the Academy's resident time-traveler.
After Vanya triggered the apocalypse in The Umbrella Academy season 1, Number Five took the Hargreeves siblings back to the 1960s, hoping to undo Earth's destruction. The mission was successful, but any consideration for the Butterfly Effect was abandoned when Allison got married, Klaus started a cult, and the gang met their own future father, Sir Reginald Hargreeves. It's hardly surprising that upon returning to their native 2019, the heroes found that not only had the apocalypse been averted, but the entire Umbrella Academy was no more; replaced by those pesky, arrogant show-offs and their pet cube, the Sparrow Academy. Adding insult to injury, Ben Hargreeves is still alive in this reality, and had been recruited into the pompous new team.
Since The Umbrella Academy season 2's final moments take place solely within the Hargreeves mansion, the audience aren't yet certain what else might've changed in this version of 2019. How much history has been rewritten? How have the Umbrella kids' lives changed? And, most curious of all, who else can Ben by coming back from the dead in season 3?
Detective Patch
By the time they each hit adulthood, the various of the Umbrella Academy (with the exception of Luther) have struck out alone. Diego is operating as a vigilante when The Umbrella Academy season 1 begins, hanging around the local police department like a would-be Batman, and while she might not have the mustache, Diego's "Commission Gordon" is Detective Eudora Patch. There's evidently some romantic history between the pair, and Eudora is torn between her feelings for Diego and her duties as a cop, while also recognizing that a man who bends knives can be quite useful now and again. When the Temps Commission send Hazel and Cha-Cha after Number Five, Eudora is naturally drawn towards the case, but soon finds herself in the firing line of Mary J. Blige. Diego is left devastated and riddled with guilt over the loss.
Since Patch's death was a byproduct of her relationship with Diego, she would surely still be alive in the alternate season 3 where the Sparrow Academy have replaced the Umbrellas. Presumably, Diego was never adopted by Reginald, and thus never met Patch to begin with. The return of a former love would bring a morbidly fascinating emotional turmoil upon Diego - meeting his revived ex only to find she has no idea who he is.
Mr & Mars Pitts
Another possibility for The Umbrella Academy season 3's new 2019 is the survival of Lila's parents. Introduced in The Umbrella Academy season 2, Lila Pitts is a Commission assassin under The Handler's care. Another of the 1989 super-powered kids, Lila holds Number Five responsible for her parents' deaths (largely because he shot them), and uses her empath abilities to gain sweet revenge against the time-hopper. But since Five's personal timeline has changed, he never ed the Commission and, consequently, didn't kill the Pitts.
There is a quantum caveat to consider with the Pitt family's possible return. The Temps Commission seem to exist outside of time - impervious to the changes wrought by time travel. In this case, mama and papa Pitt would still die, regardless of how Five's history is altered.
If the Pitts do survive, however, a paradox emerges. The Hargreeves siblings change history in 1962 with Lila's help. Reginald switches to Sparrows, so Five doesn't become a Hargreeves, doesn't the Commission as an old man, and doesn't kill Lila's parents. But without Five putting Mr. and Mrs. Pitts down during his Commission years, Lila wouldn't be present with The Handler in 1962, therefore the Hargreeves siblings wouldn't succeed in changing history. Now there's a headache.
Hazel And/Or Cha-Cha
Many Umbrella Academy followers were disappointed that the deadly duo of Hazel and Cha-Cha ween't afforded a proper role for season 2. Cha-Cha appeared to get caught up in Vanya's apocalypse back in season 1, while Hazel survived into old age, then traveled back in time to help Number Five before promptly getting killed by the Swedes. Depending on whether or not the Temps Commission are affected by timeline changes (see above) one or both of the masked assassins could return in The Umbrella Academy season 3. If Vanya doesn't end the world, Cha-Cha survives, and if the Sparrow Academy replace the Umbrella siblings, Hazel never goes to 1962 to warn Number Five, so he survives too... theoretically.
Once again, it's possible that, as Commission agents, Hazel and Cha-Cha exist outside of time, so any changes made by the Hargreeves' 1960s antics don't necessarily impact them. And similarly to Lila, a paradox is threatened because it was the lovable Hazel who helped steer the course of events in 1962 - yet by altering history, Hazel never would've been involved with the Hargreeves family in the first place.
Agnes
Sweet coffee waitress Agnes could still be alive in The Umbrella Academy's updated 2019. Falling in love with Hazel in season 1, Agnes ran away to pursue her dreams and follow her heart. The couple enjoy a peaceful life together, and Agnes dies at some point in the future, after which Hazel approaches Number Five in 1962 to deliver his warning. It was Five's betrayal of the Commission that brought Hazel to 2019 and united him with Agnes over coffee and a jelly doughnut, so if Five is never adopted into the Umbrella Academy, Hazel and Cha-Cha are never sent to chase him. Consequently, Agnes never goes gallivanting through time with her new boyfriend, and should still be alive in 2019, bored, loveless and lonely in her coffee shop. Seeing Agnes again would bring a twinge of tragedy to the Hargreeves siblings, who know she found happiness and romance with Hazel in a different timeline.
Leonard Peabody
Otherwise known as Harold Jenkins, this creepy carpenter was a big fan of the Umbrella Academy growing up, but came to detest the group after Reginald Hargreeves denied his request to their ranks. Biding his time for vengeance, Leonard seduces and manipulates Vanya into a relationship, all while coaxing out the destructive powers Reginald did his utmost to conceal. Few viewers were upset when Vanya violently turned her raging abilities onto the villainous Jenkins.
But what of Leonard in The Umbrella Academy's new timeline? Did he grow up obsessed with the Sparrow Academy? Did Reginald still reject Leonard, and now he wants revenge on an entirely different set of siblings? Or, in the absence of the heroes he loved, did Leonard just start reading Marvel and DC like the other kids? Either way, it was Vanya who killed Leonard, and in a new world where Vanya is probably a Russian swimmer instead of a superhero, Leonard could still be alive and creeping. Upon the event of his return, The Umbrella Academy season 3 could depict Leonard Peabody closer to his comic book supervillan persona, The Conductor *cue evil laugh*.
Pogo
A friend to everyone, Pogo is the loyal ape-servant of the Hargreeves mansion. A genetically engineered chimpanzee, Pogo loyally serves as the butler of Sir Reginald Hargreeves, but also brings a caring presence to the lives of the Hargreeves siblings. Complicit in covering up Vanya's latent superpowers, Pogo is one of the White Violin's first victims, pinned against the wall while the other Umbrella kids watch on helplessly. The Umbrella Academy season 2 shows Pogo in his younger years, still by his master's side, and this sets up a potential return in season 3's new timeline. Assuming the Sparrow Academy are the well-behaved soldiers they appear to be, none of them would've impaled Pogo on animal horns.
Carmichael
Debuting in The Umbrella Academy season 2, A.J. Carmichael was revealed as the head of the Temps Commission alongside the enigmatic board . Taking the form of a goldfish, Carmichael was quickly subdued by the Handler as part of her leadership coup, and some comic book readers felt this was too abrupt an ending for the scaly villain. Fortunately, Carmichael could return in The Umbrella Academy season 3. Since it's her dealings with the Umbrella Academy that trigger the Handler's fall from grace (and subsequent grudge against Commission leadership), Carmichael might escape her wrath if the events of season 1 have now been rewritten, and the whole Hargreeves debacle never happened.
Once again, this depends entirely on whether the Commission is affected by timeline changes, or whether they sit independently of the continuum, in which case Carmichael and the board would all stay dead. If Carmichael did return in season 3, The Umbrella Academy would have a second chance to turn the character into a more threatening and conniving villain, wrenching back Commission control from the helpless Herb.