Well, if you mean “which XC2 ending does XC3 start from”, then it starts from Asuka’s best ending from XC2, just as XC2 started from Asuka’s best ending from XC1.
Here are all of the XC3 endings (spoilers ahead):
(Endings are Best, Good, or Bad)
Asuka:
Best: Asuka goes overseas to America for graduate studies, and shows up unexpected on Takuya’s doorstep just before Christmas–in this ending it appears that Takuya and Asuka’s relationship has reached the point where they are just short of proposing marriage.
Good: Takuya begs Asuka not to go overseas and leave him alone, and she agrees. The ending shows Takuya and Asuka attending Natsumi’s wedding. Natsumi had planned to toss the boquet to Asuka, but Takuya caught it instead. Given that whoever catches the bouquet is supposed to be the next one to become a bride, you figure out what that means for Takuya. 
Asami:
Best: Asami is afraid of her feelings, and Takuya has to overcome this (with a bit of prodding from Asami’s mother). The ending scene shows Takuya and Asami engaged to be married, and Asami is pregnant.
Good: Takuya fails to figure out that Asami is battling her attraction for him, and asks Rumi-sensei for help. Rumi’s solution is to put the two of them together five days a week by assigning Takuya as Asami’s permanant lab assistant. The scene ends with Asami teasing Takuya–it is apparent that they both like each other but haven’t admitted it yet.
Chisato:
Best: Takuya helps Chisato to build the machine to restore her to maleness. Chisato, however, gets discouraged, worried that she really is nothing more than the stereotyped mad scientist, resulting in a major pep talk from Takuya. Finally, however, Chisato successfully completes the Quick Revolution 1031 (1031 being pronounced “tensai”, meaning “genius”–10=ten, 3=sa as in “san”, 1=i as in “ichi”). Having been built by a pair of mad scientists (Chisato and her professor), the wacky 1031 demands that Takuya answer math questions or it will auto-destruct. The first question is the area of a circle (pi*r^2). Second is the value of 1031 in base-sixteen numbers (407). Third is the value of pi…to one hundred decimal places! Takuya manages to get to sixteen decimal places before the 1031 declares that time’s up and explodes. Takuya is restored to male in the explosion, and in the epilogue we see him spending a lot of his time helping Chisato at school…and being her boyfriend outside of school.
Bad:
Because Takuya chose not to assist Chisato with building the Quick Revolution 1031, the machine is a failure. Chisato tries repeatedly over the following weeks to restore Takuya to male, but meets only partial success (the obligatory “Takuya becomes hermaphroditic” ending).
Rumi:
Best: Rumi and Takuya go out to dinner and drinking together to celebrate his return to maleness. Rumi tells Takuya about her tragic former love, who succumbed to early-onset Alzheimer’s disease in his 20s, and explains that his memory is what drives her workaholism. At the end of the evening, Rumi fakes being far more drunk than she is in order to get Takuya to escort her home, where she drags him into bed with her. In the epilogue, Rumi is going to America to finish her doctorate, and Takuya promises that he will wait for her.
Good: Rumi, Asami, and Takuya go out drinking together to celebrate Takuya’s return to maleness. Rumi does not attempt to seduce Takuya, but she starts giving him a lot more attention and help at school.
Ayano:
Best: Ayano has found an abandoned kitten whom she named Korin. Her grandfather hates cats, however, so she can not take the cat home. Takuya offers to keep Korin for her, but Natsumi demands to “play” with Ayano (in the same way that she “plays” with Takuya–i.e. very ecchi) as the price of allowing a cat in the house. Takuya tells Natsumi “I’ll let you do whatever you want to me, just let Ayano-chan go”, and Natsumi agrees. Ayano is very happy that Korin has a new home, and goes on a date with Takuya the day after Takuya returns to maleness…only Ayano’s high school aged sister Suzuno tags along to make sure that her sister’s new boyfriend meets her approval. Ayano is the ONLY girlfriend Takuya can finish with in all three X-change games in which he does not have a sex scene with her in the ending.
Bad:
Takuya fails to persuade Natsumi not to “play” with Ayano. The result is that Ayano reacts like the stereotypical real-life rape victim–she is afraid of human contact for many days afterward, especially anything male (quite a rare reaction in ecchi games).
Kouji:
Best (male Kouji/female Takuya): Kouji convinces Takuya that he really loves her (as opposed to just being infatuated), and Takuya throws away the drug that would have restored her to maleness. The epilogue shows Takuya and Kouji living together, with Kouji insisting that Takuya cook dinner wearing only an apron with nothing underneath.
Good (Male Takuya/female Kouji): Takuya decides to indulge in a little revenge against Kouji for having changed him into a girl this time around by giving him a dose of his own medicine…literally. Kouji becomes a girl and ends up getting chased around by the male Takuya. The epilogue shows Kouji deciding to stay a girl and become Takuya’s girlfriend–apparently Kouji has decided that being with Takuya is more important than being male.
Bad: Some weeks after Takuya’s return to maleness, Kouji decides to try the X-change drug on him again (the “here we go again” ending).
General Bad Endings:
Generic Bad End: Takuya returns to being male, but doesn’t get any of the girls. We see him weeks later, bogged down by schoolwork, wondering if perhaps he should have stayed a girl after all.
Maid: Takuya gets hired as a live-in maid, and gets brainwashed into being the perfect submissive servant for her boss.
Sex Slave: Takuya and Asuka, both heavily drunk from a party, get captured by a member of a sex slavery ring.
S&M Queen: While being beaten with a whip by a creepy piggish guy who had decided to make her his “pet”, Takuya snaps and grabs the whip from him. She gets revenge for all of the times that she has been forced into sex, whipping the guy until he bleeds. Finding the power arousing, Takuya, along with Natsumi, who joins in, becomes a professional S&M Queen.
