How can I find files that match a two-line pattern using grep?

So, from the comments, you're trying to get the filenames that contain an empty <cert>..</cert> element. You're using several tools wrong. As @iiSeymour pointed out, tr only reads from standard input-- so if you want to use it to select from lots of filenames, you'll need to use a loop. grep prints out matching lines, not filenames; though you could use grep -l to see the filenames instead.

But you're only joining lines because grep works one line at a time; so let's use a better tool. Here's how to search with awk:

awk '/<cert>/ { started=1; } /<\/cert>/ { if (started) { print FILENAME; nextfile;} } !/<cert>/ { started = 0; }' file1 file2 *.txt 

It checks each line and keeps track of whether the previous line matched <cert>. (!/pattern/ sets the flag back to zero on lines not matching /pattern/.) Call it with all your files (or with a wildcard like *.txt).

And a friendly suggestion: Next time, try each command separately (you've been stuck on this for hours and you still don't know what grep does?). And have a quick look at the manual for the tools you want to use. Unix tools are usually too complex for simple trial and error.