Lets assume that for whatever reason, either better Axis performance, poorer Soviet performance or dumb luck, the Germans manage to take and hold the targeted Leningrad-Moscow-Rostov line during Barbarossa. What do the Soviets do next?
As others have said, it depends on what has changed from history to allow these three "extra" victories (or two, if one counts Rostov that way). Depending on how far back
THAT POD goes, it will make a difference in how the Soviets react.
After that, the reality is even of the Germans capture the three cities, the USSR in 1941 is not going to collapse because the Germans are in the Kremlin, any more than the Russian Empire collapsed in 1814 because the French were there.
The Soviets can - and will - withdraw, trading space for time, to the east, and they have both a) winter on their side, and b) multiple river lines, including the Don and Volga to fall back on, and c) they continue to control the Caucausus and Caspian Sea oilfields, plus the resources of eastern Russia, west of the Urals, as well as all of Transcaucasia and Central Asia, much less Soviet Asia and the Soviet Far East. The Soviets also had secure - albeit lengthy - supply lines to the West via the Persian Corridor (the Iranians had surrendered in September), as well as the advantages of the winter on the North Russia Run. Lend Lease had been extended to the USSR in October, so the North Pacific Route was available as well. Kuibyshev would have functioned as the emergency capital. Stalin's position is an interesting one; I doubt he would die in his bunker in Moscow; the man had gained and held the position he held historically for a reason, and it was not because he could not calculate odds, or had a desire to die gloriously.
All else being equal, the Germans are still - presumably - in a position to launch an offensive on the scale of the 1942 summer offensive, but the basic strategic reality remains the same - every mile farther east the Germans go, the front widens and gets even farther away from the Ruhr. Odds are still strongly against the Axis being able to force a Soviet surrender.