Andre/Tony: Where they went wrong...and how I'd fix it
In 2002, "Tony" returned, claiming Stefano had helped fake his death. But this doesn't jive because Stefano had amnesia at the time and wasn't evil. Here's what I'd do...
Andre was dying of an incurable blood disease, so he decided to kill himself and frame John Black for his murder. But at the last second, he decided to fake his death. By bribing people, switching DNA tests, and using other diabolical methods, Andre faked his death.
Andre then had his body cryogenically frozen until Stefano could find him a cure. He timed the cryogenic chamber to open in six years, believing that would give Stefano plenty of time. Andre arranged for his frozen body to be stored in a high tech freezer in the basement of Stefano's townhouse in Salem, looked after by eccentric caretaker Jonesy. (In late 1997, when Vivian moved in with Jonesy, we learned there was something secret frozen in the basement but we never learned what it was. So I'd say it was Andre.) Stefano learned what Andre had done upon getting his memory back. The details were contained in a secret coded message left for him from Andre.
When Vivian came close to discovering the secret, Stefano had Andre's body shipped to a hospital in the Caribbean and pushed it to the back of his mind.
Six years later, Andre woke up. Upon learning Kristen had "died" and Stefano had never found a cure for him, Andre lost it. He tracked Stefano down to Monaco and caused a car accident. nearly killing Stefano. Andre drained most of Stefano's blood for a blood transfusion. The transfusion cured Andre of his blood disease, and he returned to Salem as "Tony" to wreak havoc upon his enemies. "Tony" was no longer dying, but the blood disease had left him nearly insane and murderous, allowing him to devise the Salem Stalker/Melaswen scheme.
Most of this stuff was stated on screen, so it's easy to fill in the blanks and have it all make sense.

