Hi Galip,
Sorry to hear about that. It looks like you're experiencing this:
https://confluence.atlassian.com/jirakb/bundled-plugin-not-available-error-thrown-on-jira-server-login-212173447.html
Follow the steps there to increase the timeout.
You may also want to review the amount of assigned memory. I've seen this is the past where it was related to low memory configurations. Check https://confluence.atlassian.com/adminjiraserver/increasing-jira-application-memory-938847654.html as a starting guide. This should be proportional to the amount of memory available on your server.
Cheers, Jimmy
It looks like there is an accepted solution to this meanwhile here:https://community.atlassian.com/t5/Jira-Software-questions/Plugin-Manager-Installation-Error/qaq-p/1542104
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