This works if you have an even number of lines after the header, as your output does (your input has an odd number for some reason):

use warnings;
use strict;

my @lines = <DATA>;
chomp @lines;
my $head = shift @lines;

print "$head  $head\n";
my $count = @lines / 2;
for my $i (0 .. $count-1) {
    print "$lines[$i]  $lines[$i+$count]\n";
}


__DATA__
a b c
0 0 d
0 1 d
0 1 d
0 2 d
0 2 d
1 0 d
1 0 d
1 1 d
1 2 d
1 2 d
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