Lochte continued to make in-roads the following the spring. He wrapped up his college career at Florida with a dominant three-event victory at NCAA's, which included breaking Phelps' newly-minted short course yards American record of 1:41.30, with a 1:40.55. Weeks later, at the Short Course World Championships in Shanghai, Lochte won three golds and set three world records, including a 1:53.31 in the 200 IM. He had set himself up to make a real run at Phelps' dominance in the event the following summer.
At the 2006 Nationals in Irvine, Lochte made his move. In the 400 IM, Lochte overtook Phelps on the breaststroke but Phelps restored order down the final 100 to ensure a one second victory. Three days later in the 200 IM, Lochte pushed Phelps down the second 100, staying with him the whole way. In the end, Phelps out-touched Lochte, 1:56.50 to 1:56.78. Lochte had pushed Phelps to his fastest time in three years, while becoming the second fastest performer in history. Still, Lochte had even more to improve. At the Pan Pacs three weeks later, Lochte surpassed Phelps on the backstroke leg of the 200 IM and led through the breaststroke leg. Phelps used a strong final turn to pull even, but the race remained a dogfight into the wall. Lochte faded slightly at the very end, and Phelps hit the wall first, finally cracking his three-year old world record. Phelps clocked a 1:55.84, and Lochte continued his break-out year with another personal best time of 1:56.11, which would have won Nationals ahead of Phelps.
As Phelps shattered his world records in both IMs at the World Championships in March, 2007 in Melbourne, Lochte could not keep race, finishing two silver medals, with a best time in the 400 IM and just shy in the 200 IM. The two men only faced each other once more head-to-head before Olympic Trials; at Short Course Nationals in December, 2007, Lochte easily defeated a recently-injured Phelps. Soon enough, the world would get the chance to see Phelps vs. Lochte part two. In an epic race to open Trials, both men broke the 400 IM world record, with Phelps winning in 4:05.25 to Lochte's 4:06.08. In the 200 IM, Phelps again narrowly defeated Lochte, posting a world record of 1:54.80, to Lochte's 1:55.22, a personal best by nearly a second. In Beijing however, Lochte could not keep pace; Phelps the 400 IMwon in another world record of 4:03.84, with Lochte relegated to bronze, having contracted a stomach flu. In the 200 IM, Phelps again lowered his world record to 1:54.23, with Lochte once again winning bronze, having taken gold in the 200 back mere minutes prior.
In 2009, Lochte finally established himself as the best IMer in the world. With Phelps passing on the IMs at the 2009 World Championship Trials, Lochte posted the second-fastest time ever at 1:54.56. At the Worlds, Lochte easily disposed of the field and broke the world record in the 200 IM, with a 1:54.10, while also winning the 400 IM. Now, with Phelps back into the IMs, a huge race is brewing in the finals of the 200 IM this evening. Lochte has a clear advantage on his backstroke and breaststroke, despite knee and groin injuries this year, and he proved in the 200 free that he is almost as good as Phelps. Moreover, his butterfly has also improved drastically since the last time the two clashed in 2008. With Phelps finally delievering a good performance in the 100 fly last night, where he posted a winning time of 50.65, just off his Olympic winning time of 50.58, he could be in-form to be in the 1:54-range tonight, as could Lochte. Neither will let the other get any advantage, no matter how fast they have to go to do so. Even Lochte's world record is not completely safe.