apparently Tony is back, as of the pilot episode.

stolen from wikipedia:
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Show-runner Howard Gordon explained that Tony's "uncertain fate" left the door open for his return[2] and cited the lack of a silent clock as a deliberate move to keep his death ambiguous. "We didn't give him the silent clock because we always wanted to keep alive the possibility for some kind of (admittedly) miraculous resurrection ... which we will explain," and followed up with "He's definitely NOT the Almeida we once knew."
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oh. dear.