Re: plugins for the site, as you've found with the Alerts plugin, sometimes make "novel" use of the database, as in making queries that the initial DB installation config never took into consideration.
In this case, I would speculate that the plugin was probably making full table scans for one or more reads or updates/inserts, which resulted in bringing the site to its knees. I'm willing to wager that a few well-placed table indexes would have resolved the issue.
Not that I'm keen on the Alerts plugin anyway, but eventually you'll add some other plugin to increase the site's utility, and when you do, testing out the queries it creates and adding indexes as appropriate would be a prudent thing to do.