Scott and Lydia kissed for the first and only time in Season 1's Lunatic; Scott was overwhelmed with sadness regarding his brief break-up with Allison as well and under the influence of the full moon occurring that evening, and Lydia, who was still somewhat of a "Mean Girl" at that time, was making a power play due to jealousy regarding Allison and her then-boyfriend Jackson Whittemore's growing friendship.
Other than this, Scott and Lydia managed to maintain a very strong friendship throughout the series. When Derek thought she was the Kanima, Derek was willing to kill her to save everyone else in Beacon Hills. However, Scott angrily told him off and refused to let him hurt Lydia. Soon, Lydia began growing suspicious of Scott and the rest of their friends lying to her, mostly in part to them keeping the supernatural community a secret. It especially concerned her because of Peter Hale attacking her the month before and Scott having Jackson, Allison and Stiles take Lydia out of school so Derek would not find her.
In Season 5, Scott's concern for Lydia was one of the reasons why he was not healing from the wound that Theo Raeken inflicted on him. However, Scott launched a full scale mission to rescue Lydia yet again. After springing her from Eichen House, it was when Scott's wound healed.
In Season 6, Scott, Malia and Lydia bonded and grew closer after Stiles was captured by the Ghost Riders of the Wild Hunt.
