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All your answers can be found in Google Webmaster Tools. Google is who removed your site and they have all the answers. You will definitely need to log into your Google WMT account to resolve this issue. https://www.google.com/webmasters/tools/ Why was my homepage kicked out from results, but not my internal pages? When Malware is detected, Google will take whatever action it deems necessary to protect their search results. If Malware was only detected on your home page, and the rest of your site is clean, then they may only remove the affected home page from the search results. How can I make my homepage appear again in the results? Step 1 - Ensure your page is free of malware Step 2 - Log into Google WMT then navigate Dashboard > Diagnostics > Malware. Run the diagnostic to confirm Google sees your site as malware free. There are many cases where a site owner believes their site to be malware free, but Google still detects an issue. Use their tools. Step 3 - One you have confirmed your site is fine then click "Request A Review". Google will then confirm your site is malware free and can remove any warnings they have placed on your site. Step 4 - Once your site is cleared, you can then submit a Reconsideration Request. Expect the process to take a month. The last time I experienced an issue it took a solid 3 weeks. From what I have heard that is better then average. Best of luck.