Is it permissible for someone who prays some of the congregational prayers in the mosque to combine prayers due to rain?

If the reason permitting the combining of prayers (jama') is present, then performing it is permissible. Their praying combined in the mosque, when the condition for combining is met, is more befitting than praying in their homes, because "abandoning combining while praying in homes is an innovation contrary to the Sunnah." And the Sunnah is for the five prayers to be prayed in the mosques in congregation.