As I suspected, Gridman Universe puts Gridman Universe solidly among the top 3 strongest Trigger series, with only Gurren Lagann and Kill La Kill posing any competition. The reason people from other worlds are appearing is because there's a multiverse (by common series plotline, Utsumi means of Ultra series; Gridman Universe's writer Keiichi Hasegawa was even the main writer of several Ultraman series, including Ultraman Nexus).
The core threat, which causes the Dynazenon cast to appear in the SSSS.Gridman universe is believed to be a Big Crunch on a dimensional level...
...However, it ends up being something else; Gridman was forced to engulf the entire Universe by an unknown force, which caused the Multiverse to overlap, which includes all of the universes that Gridman created (being able to create is an ability that Gridman gained from humans, as he has no form originally), thus threatening all of existence.
As Gridman would never want a situation like this to happen, the only conclusion is that Gridman is being controlled (which turns out to be true, as detailed further below).
When Gridman's consciousness shuts off in the world Akane created, all the cast of Dynazenon (with the exception of Yomogi) vanish. Knight (who reverts to being Anti) says that Yomogi was able to survive because of Anti's acceptor and Yomogi's strong connection with kaiju.
Yomogi has an existiantial crisis about his world and the lives of everyone he knows and loves being a creation of Gridman...
...To which Rikka, Utsumi and Yuta point out they are creations of a goddess called Akane Shinjo, and have even been called artificial creatures; the fact that they're artificial doesn't matter as they're still people with thoughts and feelings and lives. The Second says that humans are the only lifeform to believe in things that not only have no physical form, but may not even exist (feelings, relationships, myths, laws, national boundaries, etc).
The Second says that Yuta must perform the Access Flash with Gridman, but warns that for a normal human to perform the Access Flash with an infinite Gridman would mean loosing themselves.
Yuta performs the Access Flash...and ends up in a dark void beyond the world he came from. He speaks to a enigmatic goddess, who takes the form of a live-action girl, who shows him the Gridman Universe; this is Gridman overlapped with the entire Universe (which contains not just one but many universes), and he's fragile in this form and about to break apart. He still makes the form of the Universe into his own form, as an SOS signal. Yuta must save Gridman before he breaks apart.
This mysterious figure is none other than Akane Shinjo in the real world, who after sending Yuta on his way, performs an Instance Domination to control Alexis Kerib (who's been kept prisoner by Gridman for his crimes). This means that Akane still has powers even in the real world.
Akane pilots the now-heroic Alexis Kerib, who flies along the length of the Gridman Universe in seconds (which contains multiple universe and is described as being infinite).
At last we discover the sinister force behind everything; Mad Origin, an entity in the form of a kaiju collective created from all the kaiju created by human emotions across the Multiverse (to which Akane admits some fault in that part); the Mad Origin may not even be truly conscious, just a replica of human emotions.
Mad Origin seeks to use Gridman to destablize the cosmos by trapping it in Gridman's form, which would lead to the destruction of everything.
Alexis Kerib shatters the Mad Origin's red bubble, which after Yuta's own actions to free Gridman's consciousness, frees both Gridman and the Universe (the red sphere around Mad Origin is big enough to be seen next to Gridman Universe, and even its shards are visible). Both Gridman and Mad Origin end up back in space and back on Earth (after Gridman blasts Mad Origin there).
Alexis Kerib is being controlled by Akane Shinjo from another dimension.
Struggling against Mad Origin, Alexis Kerib uses Instance Abreation to materialize the universe(s) inside Gridman's head, restoring the Dynazenon cast, who come to Gridman's aid.
During the fight, Mad Origin is able to predict all of Gridmans moves as he knows all of Gridmans move (from the perspective of the kaiju).
Mad Origin merges with Alexis Kerib by eating him, and Gridman, Dynazenon & Knight defeat Mad Origin by combining destructive and healing power (Alexis Kerib may or may not be permanently dead). Everyone then goes to their own universe, and Yuta finally asks Rikka out.
Retroactively, this would confirm that Computer Worlds are infact universes (at minimum), so Gridman destroying Khan Digifer and surviving Takeshi's computer world being destroyed is a universal feat (at least; Khan Digifer also took over all the computers worlds on Earth so it's potentially multiversal. I'm not sure if the real world is a part of Gridman Universe or not (there's a line from Alexis which implies Akane's world is beyond even the Gridman Universe, as he refers to her returning to 'this world' even when they're in the white void outside Gridman Universe (also on this note, when Takeshi's computer world was destroyed in Hyper Agent Gridman, all that was left behind was a white void).
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