Keep the two eras separate
Google introduced Penguin in 2012 to address link spam. In September 2016, Google announced that Penguin became part of its core algorithm, refreshed in real time, and became more granular by devaluing spam based on signals rather than demoting the ranking of an entire site.
Google's current ranking-systems guide now lists Penguin as a retired named system that was integrated into the core systems. A current loss can involve link spam or link-value changes without creating an observable “Penguin 4.0 penalty.”
Look for link creation, not merely ugly domains
Start with how links were acquired. Paid placements meant to pass ranking credit, automated networks, reciprocal schemes, and controlled sites built to link are stronger evidence than a vendor's domain metric. Review invoices, vendor reports, anchor patterns, target-page selection, and abrupt creation periods.
Search Console's Links report is a sample, not a complete ledger. Combine sources, but keep the distinction between an observed link and a claim that the link harmed rankings.
Use the manual-action branch when it exists
If Search Console reports unnatural links to the site, follow Google's manual-action process: stop the scheme, seek removal where possible, document the work, and use the disavow tool for qualifying links that remain. Then request review with the completed evidence.
If the report is clean, there is no reconsideration request. Fix link acquisition that violates policy because it is a continuing liability, but do not promise that one file upload will reverse an algorithmic loss.
A link loss may be exactly what it looks like
Rankings can fall when valuable links disappear, pages that linked are removed, or links stop being counted. That is not necessarily a punishment. The site may simply have less support relative to current competitors.
The useful response is to restore the reasons real pages should cite the site: original resources, products, reporting, tools, relationships, or genuinely useful work. Penguin history explains why manipulative acquisition is fragile. It does not remove the need to earn current relevance and recognition.