Here's a run-down of the Fate/Extra retelling that Extella continues from:
Hakuno (Male) is the protagonist and Nero is his servant.
There's a generic female NPC who interacts with both Hakuno and Leo quite often.
A mysterious burned Servant shows up and helps out Hakuno for unknown reasons.
The first three boss battles happen the same as the PSP game (Shinji/Drake, Dan/Robin Hood, Alice/Nursery Rhyme).
Instead of a Rin/Rani route split in Chapter 4, Hakuno's next opponent is an Extra version of Atram (Medea's Master) and Caster Tamamo.
Atram is the exposition guy for the state of the Extra timeline's Earth. Still a dick in this timeline regardless.
Tamamo is left behind as a scapegoat and Atram escapes death - either the Moon Cell or Julius take him out.
Hakuno uses a Command Seal to contract Tamamo as a Sub-Servant to prevent her from disappearing. Nero's hopes for a Mana Transfer are dashed away by a foxy waifu.
[*]Fifth round remains the same. Fate/Extra CCC occurs after this.
[*]During the sixth round, Rin and Rani are eliminated. Hakuno assumes that he'll be going up against Leo - but it turns out that Leo's also been eliminated.
[*]Seventh round opponent is Hakuno (Female) and Archer (EMIYA).
She disguised herself as the generic female NPC and her existence is linked to Hakuno's. When he develops his ego and becomes an individual, she does so as well.
There can only be one Soul, however. Hakuno (Female) is destined to fade away/die/self-destruct without it.
Archer helps out Hakuno (Male) because if he dies then so does his Master. He's aware of her situation and wants to bring her as far as he possibly can before the inevitable.
FemHakuno and Archer lose and disappear. Hakuno inherits her memories and we get the Leo fight from her perspective.
[*]When they arrive at the Moon Cell, Tamamo gets removed via a Bug Check since she's a defeated Servant who shouldn't be there anymore. Don't worry, she's fine and back in Extella. Final battle occurs as normal with just Saber.
I actually like Nasu's crazy fanfiction version of Extra and I'm thoroughly disappointed that SHAFT is probably going to do FemHakuno and Nero in a straight adaptation of the game. At least we have Apocrypha to look forward to.