I'm tagging this as Hooked Queen, and Swan Queen, because ultimately Swan Queen is the endgame romance.
When Emma leaves (Midseason 3), Regina finds herself with longing and missing, not just Henry, causing her pain in her heart, but also Emma. Unable to admit to herself her feelings for Emma, she looks to Hook for comfort. Hook, also upset Emma is gone, after sharing their kiss in Neverland, The Queen and the pirate share drinks, and one night in bed.
Unable to cope, without Henry, and Emma, Regina asks Hook to go find her in NY with a memory potion to bring her back. However, a curse happens, sending everyone back to SB, Hook is able to outrun it and get to Emma in NY.
When Emma returns, Regina is with child... Killian's child. See how they work through it, deal with the Wicked Witch threatening the baby, and who admits their love.