As phase 2 runs a shell command, I assume the server is running on Linux. Put an ampersand character after the server run command to put the process in background:
run_server &
and phase 2 will complete as soon as the server is launched. You'll probably also want to send the server's console output to a file, e.g.
run_server > server.log 2>&1 &
(the 2>&1 sends stdout and stderr output to the same file)