Good point, Umaro. That puts two Januses in the Keystone Timeline (not counting the dimensional split for obvious reasons).
Janus A - Travels with the party. Meets his double from an alternate future, where Lavos has already fallen.
Janus B - Alternate-Future Janus, who is seen in Time's Eclipse. Entered Time's Eclipse from a timeline where the Time Egg was received from Gaspar, but is ultimately not used to resurrect Crono. Janus B discovers that Schala is alive as RD Kid and becomes "Magil Of The Shadows" so he can watch over her. After the Viper Manor Incident, in which Kid discovers her identity as Schala, he helps her get on her feet, and then goes back to prevent her from ever becoming Kid. He winds up in Time's Eclipse, and meets the party, which has his past self (Magus) among them. He leaves them behind to defeat the Dream Devourer on his own, and is defeated. After the party fails to defeat the Dream Devourer and is sent away by Schala, he confers with his older sister, who knows who he is, before also being sent away. he realizes his efforts are in vain and resets himself, erasing his memories, personality, all of it.
Janus A's fate - wanders the Period Of Antiquity in search of Schala, not remembering what happened at Time's Eclipse.
Janus B's fate - wanders the Present with amnesia. Becomes Guile, the mysterious magician. Joins Serge in destroying the Time Devourer.