Tokyo uses two rail networks: the Tokyo Metro and the Tokyo JR lines.
As both seldom overlap, TTDIT suggests that you download both for convenience.

TOKYO JR LINES

jr
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TOKYO METRO

metro
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RUSH HOURS / CROWDED HOURS

7:30am to 9:30am
5:00pm to 7:00pm
9:00pm to 11:00pm
Last train time for big stations

At those times, main lines and stations are very crowded.