This year's crossover was basically a set up for a huge DC event from the comic books, "Crisis On Infinite Earths", which will be the crossover for Fall 2019.
"Crisis On Infinite Earths" is the event in the future newspaper article that causes Barry Allen to go missing (and never return).
Explanation of events of the DC tv series crossover...
"The Monitor" is a good cosmic being that is going from earth to earth changing reality to test the heroes of each earth so he can find a earth that has heroes that are able to defeat "The Anti-Monitor", who is an evil cosmic being that is coming and will be trying to destroy all the earths in the multiverse.
The Monitor is shown on Earth-90 and we see all the various heroes are already dead, except The Flash, who confronts The Monitor but escapes that earth before The Monitor uses his book to destroy that earth. Earth-90 is the earth of the 1990's The Flash TV show, along with the Smallville TV show (we see Smallville's Green Arrow among the dead).
The Monitor comes to Earth-1 and gives the reality altering book to some deranged doctor who works at Arkham Asylum so that doctor can mess up reality and Earth-1 heroes can rise up to stop him and be tested by The Monitor.
The first time the doctor is given the book, he tries to give himself The Flash's powers, but he messed up and it ended up switching Barry Allen and Oliver Queen into each other's lives. Barry and Oliver decide to find Supergirl on Earth-38 and see if the switch is limited to their earth or it affects all earths. Supergirl can tell who they are, so it is limited to their earth, and she returns to Earth-1 with Superman and they fight Amazo (a robot that is infused with a special drug from past Arrow episodes that allows it to scan and copy DNA, basically allowing it to imitate super powers).
The gang gets a lead, that the doctor is somewhere in Gotham City (because of Cisco's vision). They go to Gotham City where they cross paths with Kate Kane, Bruce Wayne's cousin, who offers to help them out so they will finish whatever they are there to do and get out of Gotham City.
They find the doctor at Arkham Asylum and are able to get the reality changing book away from him.
Cisco, Caitlyn and Felicity figure out that the red skies and yellow lightning storm happening is Earth-90 Flash trying to breach to their earth but he doesn't have the strength to make it here, so they create a device to help him. Earth-90 Flash finally makes it and explains most of everything that I have already written here.
They find The Monitor and confront him. The Monitor zaps Earth-90 Flash back to where he came from. The Montior explains that he is impressed by Flash, Arrow, Supergirl, because this is the first earth where the heroes actually figured out the importance of the reality changing book AND were able to get control of it. The Monitor then steals the book back.
The Monitor gives the book back to the doctor and tells him to think bigger and the doctor warps reality again, this time taking away Barry's and Oliver's powers and making himself Black Superman (who he only knows about from Superman's participating in the fight against Amazo). Barry and Oliver use their wits to escape, they end up finding the reality warped version of Cisco and breach to Earth-38 to get the original Superman.
They end up getting the book back and Superman uses it to restore Barry's powers and Oliver's talents. Black Superman (the doctor) ends up getting the book back and starts messing with reality again. Oliver has a plan but needs the other heroes to buy him some time, and Barry comes up with the idea that if he and Supergirl go around the earth fast enough they can slow down time (homage to 1980's Superman movie) eventhough he is told that he will die by doing so.
Oliver confronts The Monitor and finds out that The Monitor isnt looking for heroes with great powers. He is looking for heroes with great values and is impressed that Flash and Supergirl are willing to die to save the earth. The Monitor offers to save Flash and Supergirl but states that saving them would tip the balance and what would Oliver be willing to offer to save Flash and Supergirl.
Oliver is next seen with some weird arrow (that he likely got from The Monitor) that disables the reality warping book. Supergirl goes home. Barry and Oliver talk in a bar and Oliver makes a toast "To enjoy what you have... as long as you have it" (implying that Oliver made a deal with The Monitor for Earth-1 heroes to fight The Anti-Monitor, and likely that Oliver will now be the one to sacrafice himself and disappear instead of Barry... aka Crisis On Infinite Earths)
Smallville song is "Save Me" by Remy Zero https://www.youtube.com/watch?v=LYdCzs5uPrI