Primoz Roglic (LottoNL Jumbo) spoiled the party for Team Sky by escaping to victory on the final ascent to take his first win of the season, with Adam Yates (Mitchelton-Scott) securing second on the day. Neither Roglic nor Yates were a threat on GC and Thomas now leads Greg Van Avermaet (BMC Racing) on count back, with Chris Froome (Team Sky) in third, at three seconds.
With two back-to-back stages ending in climbs still to come, Thomas is well-placed along with Froome and Michal Kwiatkowski. The Pole is fifth on GC and after winning the Volta ao Algarve earlier in the season is a genuine contender for Tirreno-Adriatico in his own right.
Team Sky, as Thomas said during his post-stage press conference, have options.
"With three of us in a decent position, hopefully one of us can do it," he said, before pointing out that Team Sky has never won Tirreno-Adriatico.
"Saturday is the first long mountain finish and it's the first one I and Froome will have done this year. We'll just see how the legs are. We were both unsure of how we were before today but we're both going well. I'd love to keep the jersey but if I don't have the legs hopefully he can take over. It's going to be a big, big test.
"I knew that Roglic was going well. He was in Tenerife when we were there. He's quite a way down on GC, so it wasn't a major threat on GC [when he attacked - ed.]. We still wanted to go for the stage but he was strong and he got a good enough gap. The climb was only a three-minute effort so tomorrow will be different. It's good that we have options there."
Saturday's final climb to Sarnano Sottotetto is the hardest of the race and ends with the 13km ascent at an altitude of 1,335 metres. The effort will be an utterly different one to the venture Thomas and the rest of the peloton powered up on stage 3.
"That was the first effort I've done like that in a while. That was hard. It was all about getting numbers over the first time we did the climb and then having a good position at the bottom. To be honest, I didn't feel great but I don't think anyone did," Thomas had told Cyclingnews almost immediately after crossing the line.
At the start of the stage, a tentative Thomas was unsure with regards to his form. Algarve, despite a podium, is not the same race as Tirreno, where the field is deeper and the terrain harder.
"I'm a bit unsure how I am and Froome the same. We'll just see after today. I feel okay but I don't quite feel like I did last year. This is quite a step up from Algarve and the training has been going alright. I'm just a bit heavier than I was this time last year. That's all with July in mind. I'm around 70-71kg and that's not bad."
Thomas' July plans essentially rest on the future of Froome, with the Tour champion's participation resting on the fate of his salbutamol case. Thomas has spoken of his desire to have his own chance at the Tour but he is also down to ride the Vuelta a España. When asked if he could lead in Spain, the Welshman downplayed his chances.
"I'm down to ride it but I'm just not sure about GC. I want to be in my best shape for July and I don't think that I can go for GC in two Grand Tours in a row. It takes so much for me to try and be good, with all the sacrifices for July … never say never and I'll try and stay on top of the weight. That's the biggest thing for me. The weight. Then obviously physically and mentally, after three weeks of tough racing. It's all up in the air and we'll see. I'd like to go there, whether that's for stages or to help. We'll see. It's a long season."
With the leader's jersey on his shoulders, Thomas could at least talk about racing. The last few weeks have seen Team Sky under severe pressure do the DCMS report, allegations surrounding corticoid use – which has been denied by the team – and Froome's ongoing case.
"It's nice to talk about something else other than Brad [Wiggins] and what went on back then. It's nice to get on with the race and like I've said before, I just worry about myself and have been in my own little bubble, and working hard. I'm just trying to be in the best shape possible for races."