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What happened in the end? My evil mother made me miss the last 5 eps! gonk

*sigh* why is it no one answers my questions??? crying

When you wish...

... Upon a star.

Gah, what a vague summary you gave. D:

For the last few episodes...

Morganna began to target Subaru to get to Tsukasa's weakness. Helba began to assist them, offering Net Slum as a temporary safehouse, since Morganna could not find Net Slum (since the server was created independantly by Helba). They rallied together before they took action. Sora had one final moment of betrayal to the main characters, being defeated by Crim, before retreating temporarily.

Morganna locates Net Slum, and sends Macha and a Guardian to destroy Subaru - Tsukasa's only hope - and Tsukasa defeated Morganna's Guardian with his own, both of the Guardians negating one another. Macha leaves.

When they leave Net Slum, they go to Hidden Forbidden Holy Ground (the church) and encounter another Guardian. After a long time, Tsukasa resolves to stay and fight for once, and the party manages to defeat one Guardian. Three more appear. Before they begin fighting again, Macha appears, and allows to get herself Data Drained by the Guardians, taking them with her. The grass she recieved from Tsukasa a few episodes prior blooms as she dies - becoming Enokoro-gusa (literally translated, foxtail grass, but known as Aromatic Grass in the dub). If you watch her death in Japanese, you can hear her screaming. The voiceactress was not creditted.

Morganna captured Mimiru, Tsukasa, and Subaru, and separated them in a vast desert. She showed them AIs based off of their friends, confusing them with hateful words. It didn't take long for them to find one another and realize what happened, but there wasn't much time to stall. The three were then taken to the second place Morganna held Aura.

Small events occured, but led in Tsukasa, Mimiru and Subaru locating Aura. Morganna scolds Tsukasa, threatens him, bribes him, tries her hardest to keep him from awakening Aura. Tsukasa scoffs, and realizes that he's not afraid of her, and not afraid to go back to the real world. This strong emotion awakens Aura, and Tsukasa takes her with him when Sora betrays and stalls Morganna. In anger, Morganna Data Drains him and turns him into Skeith. In the real world, fourth grader player of Sora falls into a coma from which he shall never wake.

Tsukasa and party bring Aura to Net Slum, and are cut off by Skeith. Before they get into a fight, Helba shuts down the server, gambling Tsukasa's and Aura's existance. If it failed, Tsukasa and Aura would both be lost. Fortunately, they both survive - Aura existing elsewhere in The World and Tsukasa freed from the hospital. Tsukasa and Subaru reunite, pleased to see each other again...

...but, to forshadow the plot of the games, Morganna's voice appears once more, repeating her most famous line, "I have been waiting for you for a very long time. I need you as much as you need me. So long as we walk together, I shall protect you..."

And there, the series of SIGN ends, and the baton is passed to the INFECTION series, the story carried on...

Wait what? Sora does not become Skeith, Sora becomes Skeith's wand. You can pretty much say Sora was Skeith's original "Epitaph User", except he isn't really in control.