Todd, who has ridden Conair only once before, finished clear with just 2.4 time penalties. Todd last won at Blenheim when he guided Land Vision to victory in the CIC three star in 2010.
"Blenheim is a proper three-star track this year - perhaps a bit bigger than it has been recently - and that's a good thing as it will set horses up well for Badminton," said Todd, who admitted to a few "hairy moments" out on the course with Conair.
Nicholson's hopes in the CCI three star went wayward after he and Viscount George had a refusal and retired.
Jonelle Richards and Mere Oak moved up the leaderboard with a clear round and 9.6 time faults to sit in 14th place. Dan Jocelyn and Special Advocate moved up five spots into 25th after a clear round with time faults, while Jonelle Richards and The Deputy slid 11 spots after a refusal and time faults. Juliet Wood and Bold Trader rode a clear round to pick up only time faults.
The cross country in the CCI three star will run tonight, with the showjumping of the CIC three star also scheduled to go.
Results -
CCI three star (after dressage and cross country phases): William Fox-Pitt (GBR) Seacookie 39 penalty points 1, Mark Todd (NZL) Conair 42 2, Kristina Cook (GBR) De Novo News 42.8 3, Jonelle Richards (NZL) Mere Oak (owned by Lucy and Ben Sangster) 55 14, Dan Jocelyn (NZL) Special Advocate 63.2 25, Jonelle Richards (NZL) The Deputy 67.8 29, Juliet Wood (NZL) Bold Trader 72 37, Lucy Jackson (NZL) Kilcoltrim Ambassador (owned by the Sprout Syndicate) 81 43, Neil Spratt (NZL) Elton II 144.2 64, Caroline Powell (NZL) Thornfield Jones eliminated in the cross country, Lizzie Brown (NZL) Henton Attorney General eliminated in the cross country, Andrew Nicholson (NZL) Viscount George (owned by Robin and Nicola Salmon) retired in the cross country.
CIC three star British Championship class for 8 and 9 year old horses (after dressage and showjumping phases): Andrew Nicholson (NZL) Quimbo (owned by Deborah Sellar) 35.1 penalty points 1, Piggy French (GBR) West Side 39.3 2, Bettina Hoy (GER) Designer 10 40.8 3, Caroline Powell (NZL) Onwards and Upwards owned by Cameron and Mary Crawford and Powell) 52..2 19, Mark Todd (NZL) Leonidas II (owned by Diane Brunsden, Peter Cattell and Todd) 52.4 20, Jonelle Richards (NZL) Wesko (owned Christina Knudsen) 55.5 25, Lizzie Brown (NZL) Playtime NZPH (owned by Chris Ellis) 70 57, Neil Spratt (NZL) Fernhill Quality Street 76.8 63.