Credits to AlanSpacer from Beast's Lair:

-A lot of Extra and its part of the Fate multiverse has been tied/retconned to Extella. For example, the entire reason for the Mooncell grail war and therefore all the games' events was to find the strongest champion for the Mooncell to inherit the Regalia, which gives a person all the knowledge and power of the Mooncell (like the Sysadmin), so that THAT person can defend it against Sefar and other Velber incursions. The Mooncell gives off a kind of cloaking field to our entire solar system, earth, etc., so it being up and running prevents the Velber star from coming to find us again and therefore destroy everything.

-At its core, G.Altera/Sefar/Velber 02 and its cronies are DIGITAL lifeforms. What crashed into the moon is a photonic crystal ship, in which's 'cockpit', which isn't really a physical place is the Altera core. The only physical thing is Earth!Altera which it spawned as a linked avatar in the real world to grow and destroy the planet the first time they showed up. It's basically a TYPE. Nothing of earth can hurt it, not like, its SO strong, more like the concept of hurting it doesn't exist, regardless of the weapon, concept, or strength used. It has no concept of death, etc. G.Altera/Sefar killed ANYTHING that fought it, Gods, TYPES, spirits, heroes, Humans, nature, Gaia, it can absorb the mana of anything and use it to grow. The only thing that could stop it was the 'mysterious hero(ine) X', identity unknown, who wielded what was definitely Excalibur (same description though not named) and killed it after it destroyed 80% of the planet. COMPLETELY destroyed 80%, raized to waste. Absolutely zero info on who it was that wielded it, but they WERE Human.

-As an aside to the above, the reason Gil "owes Altera a favor" and hence helps out, it's not a personal favor, it's because in the EARTHOCIDE past Sefar spared Gil's forebearers. Gil actually is helping out (tsunder'ily) mostly for Hakuno, but he does pay off his 'debt' to Altera herself. This comes into play in Altera's Route big time when he saves them from Archy winning.

-Because Earth!G.Altera died, the Mooncell one shutdown from the feedback and was able to be sealed in her Chamber of Stone 'cockpit' virtual space for millenia. Archimedes is another digital Servant of Velber who is trying to fulfill the programming of destroying the Mooncell using Sefar or otherwise so that Velber can find its way back and finish the job. He has set up a quantum timespace loop within the domain of the Mooncell where he's basically trying again and again from the start of Extella's events to the end to awaken Sefar from Altera and destroy the Mooncell. At first, he's the only one who retains his memories. He's playing a giant con game against everyone, since he plays the good guy/infodump guy, so he's a bit like Kotomine. So he's always telling the other teams and/or your team that "THEY'RE the villains, do what I say and it'll make everything BETTER!" Example of his 'looping planning': In Nero's route he infects Liz with Void Cells, corrupts her, but her Mooncell virtual body can't take the power, so she fails/dies. So in Tamamo's route he strengthens her body with Void junk too, but she still goes crazy and corrupted and so turns against him. Etc.

-Hakuno, in order to escape Archimedes/Altera's cluthes, splits himself into mind, body, and soul, and thus has fragmented memories, identity issues, etc., which adds on to the chaos of Archimedes trying different things based on how he fails in the three timeloops you see. Since there are three Hakuno's running around in each route with their own fragments of loyalty and emotion and memory working with Nero, and Tamamo, who are rivals and fucking with each other, and Altera/Attila, who is actively their enemy in taking down the Mooncell, although not liking it and not working with Archimedes, which makes it even more confusing. So that Hakuno is technically a villain. Altera's route sees him and Altera kill Nero and others and actively oppose the "good" aligned him/herselves. This is worsened because Altera's Hakuno is the 'body' Hakuno, and the other two will die if he dies, if they haven't refused with themselves at least.

-In all three timeloops you go through (before the 'true' final loop), Altera is reawakened into Sefar by Archimedes buckfuttery. Remember, that each Hakuno is going through all the My Room and bonding events and adventure with their Servant, on top of their vague memories and emotions, so think of each Hakuno as an equal protag with love ties to their Servant as in any Route, despite competing against each other.

    • In Nero's ending, whose route is a pretty straightforward 'adventure' to stop the 'evil' forces of Sefar/Velber, you do, but Body Hakuno, who is just as tightly tied emotional to his Servant, Altera, commits seppuku, bringing the others with him.

    • Tamamo's route's theme is entirely "I am an immortal god who dealt with Mayfly romances, and on top of that I KNOW the Velber will probably be back in the system someday soon with Sefar, and nothing can stop them. I saw the destruction of the world millenia ago, saw everything die to Sefar02, and am hopeless." So, trying to ignore that truth and just enjoy the 'last' days of happiness with her Hakuno as best she can, she tries way too hard to overcompensate and generally messes with everyone while trying and failing miserably to love-love. In the end, Hakuno gives her a "but we can beat them here in the Mooncell, it's not like the actual old Earth rules apply' speech, powers of love and hopes her up, and they have a relatively happy ending.

    • Altera's route is all about 'working with the enemy', and then 'falling in love with the enemy who is a literally giant sweetheart who wants to be Human and ignore her programming/mission and doesn't want to destroy all civilization, but inevitably can't" kind of thing. While Archy muck everything up and turns the others (somewhat rightfully) against you by playing them. After dealing with all the other Servants and whatnot, Archy kind of separates Servant Altera and G.Altera using haXX0ring and sysadmin junk, reawakens Sefar anyway, and when Altera kills it they both die. Hakuno uses the Regalia to find out about the timeloop shenanigans and all the knowledge that Archy has been privilege too over his multiple attempts (the various routes), and goes back to transmit his memories in time himself to prevent the whole thing. He succeeds but dies doing it.

-The final, 'true' route: Since it goes back to "the beginning", Hakuno is with Nero, who was his main Servant in the AU of Fate/Extra that lead to Extella, and is the final MC. Now that the various MCs know the truth they can 'not believe ArchyOndore's lies' and just like any good timeloop story can just stop the problem(s) from the very beginning before they start armed with their forewarned knowledge. So they kick the spitlickins out of Archy from the very start and go to team up with Tamamo and co. By the end, using the Regalia and the Mooncell, and with Altera actually working with them and against her nature, eventually passing on her powers to Nero to create Saber Venus super apotheosis form, she actually takes out the core of the Sefar/Velber shite permanently and removes Archy's time shenanigans. Altera is 'reborn' as a loli daughteru and they live haremly ever after. There's the vague notion that Velber might return in this or other Extra reality versions to be a right prick again.