Kanashige ni saku hana ni kimi no omokage o mita
daisuki na ame na no ni naze ka kyou wa tsumetakute
    Within a flower bloomed in grief, I saw an image of you
    Even though I love the rain, for some reason today it seems cold

Awaku hakanaku yoru ni yurarete tameiki hitotsu ochita hanabira
    Wavering in the transient uncertain night, a solitary sigh, a fallen petal

Tsuki no kakera o atsumete yume o kazari nemuru
toki no suna chiribametemo ano koro e kaerenai
    Collect the fragments of the moon, sleep decorated in dreams
    Even if the sands of time are scattered, we can't return to that time

Futo miageta hoshizora mata kimi o sagashiteta
ikutsu yoru o koereba namida wa "tsuyosa" ni naru?
    In the starry sky I looked up to by chance, again I was searching for you
    How many nights do I make it through, before my tears become "strength"?

Kisetsu wa meguri mori wa somerare kaze wa kanadete omoi afurete
    The seasons pass by, the forest is dyed, the wind sings, the memories overflow (2)(3)

Aitakute itooshikute furetakute kurushikute
todokanai tsutawaranai kanawanai toosugite
ima wa mou kimi wa inai yo
    I want to meet you, lovingly, want to touch you, suffering
    Can't be sent, can't be told, can't be granted, too far away
    You're not here anymore

Chiriyuku to shiru hana wa sore demo tsuyoku ikiteru iroazayaka ni
    Knowing it will scatter and die, despite that the flower strongly lives on, in bright colours

Tsuki no kakera o atsumete yume o kazari nemuru
toki no suna chiribametemo ano koro e kaerenai
aitakute itooshikute furetakute kurushikute
todokanai tsutawaranai kanawanai toosugite
ima wa mou kimi wa inai yo
    Collect the fragments of the moon, sleep decorated in dreams
    Even if the sands of time are scattered, we can't return to that time
    I want to meet you, lovingly, want to touch you, suffering
    Can't be sent, can't be told, can't be granted, too far away
    You're not here anymore

Notes;
1) While this song is essentially the opening theme for Black Jack the lyrics are different in the second half. On the single itself, the third track is the actual opening theme, but JDA decided not to print the lyrics for the "Black Jack version" for whatever reason.
2) by "pass by" it's meant that the seasons are 'encountered'
3) the verb used with the wind here actually means to be played like a musical instrument