Reading through the Cat And into the forest i go to lose my mind and find my soul shirt, and my own ideas from playing, id think you were captured maybe a day before ulfric and his men. ralof says they were ambushed in darkwater crossing, while you were crossing the boarder from cyrodiil. the imperials probably thought you were an estranged stormcloak trying to get information out of, or into, skyrim. my guess is that lokir had stolen an imperial camp’s horse, which is why he was caught up in the mess. he was probably caught right around the time you were in the south, nearest the boarder.
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They took your belongings to make sure you didnt have any information on you, like Cat And into the forest i go to lose my mind and find my soul shirt if you were an undercover courier, and they didnt bother letting you keep your clothes or other belongings if you were going to die anyway. another imperial group from the north met up with the southern group to have the stormcloaks executed with any other prisoners. easier to kill two birds with one stone- in the same nest (helgen). ralof saying “you were caught up in that imperial ambush, same as us.” probably doesnt immediately mean that you were near darkwater crossing, but that you were also caught up in an imperial ambush, since they were too. both of you unlucky enough to be caught in a mouse trap, even if they were different traps.