Let's say the Swedes win a very decisive victory at the Neva in 1240. Alexander Nevsky dies (probably known ITTL simply as "Alexander"), the Novgorodian army is routed with very heavy losses.

Now, contemporary sources claim the Swedish aim was the conquest of Novgorod, but that is obviously not realistic. But they will now definitely control the mouth of the Neva and Ladoga, which probably severely weakens Novgorodian trade.

What happens next? I assume the Teutonic Order will still try to expand to the East, would such a weakened Novgorod be able to resist? If not, how far can the knights go? Coupled with the Mongol invasions, what would this mean for Russia as a whole and Russian Orthodoxy in particular? Could Novgorod be gradually conquered and Catholicized?
 
Let's say the Swedes win a very decisive victory at the Neva in 1240. Alexander Nevsky dies (probably known ITTL simply as "Alexander"), the Novgorodian army is routed with very heavy losses.

Now, contemporary sources claim the Swedish aim was the conquest of Novgorod, but that is obviously not realistic. But they will now definitely control the mouth of the Neva and Ladoga, which probably severely weakens Novgorodian trade.

What happens next? I assume the Teutonic Order will still try to expand to the East, would such a weakened Novgorod be able to resist? If not, how far can the knights go? Coupled with the Mongol invasions, what would this mean for Russia as a whole and Russian Orthodoxy in particular? Could Novgorod be gradually conquered and Catholicized?
The main problem with a premise is that, AFAIK, there is no trace of that expedition on the Swedish side and it seems that on the Russian side its first mentioning is in the chronicle of the XIV century and is void of any meaningful details (how is it likely that the name of the Swedish leader was “Spiridon”?) and the “classic” description of the alleged battle belongs to the XVI century and seems to be a part of the PR campaign promoting Alexander as a founder of the Muscovite ruling dynasty. This source is seemingly the first one which uses nickname “Nevsky” (depending upon the source, this nickname either was given to different prince of this name or was referencing to the estates that Alexander and his family owned on the Neva River). So there are no contemporary sources on either side related to this alleged event.

Realistically, there were numerous small-scale border raids conducted by all regional entities so some skirmish could happen

As far as the trade was involved, Novgorodian international trade started in X-XI centuries and during that period the closest trade relations were with Norway. In the XII the main partner was Gotland and starting from the early XIII the Hanseatic cities. In other words, there was no interest on any side involved to cut or minimize the existing trade and, as later experience demonstrated, the Novgorodian merchants had been quite happy with a schema in which the foreign merchants had been coming to Novgorod to buy and sell their goods. Novgorodian part started with carrying the goods from the coast to Novgorod by the boats (and getting paid for the service) and ended with carrying the purchased goods from Novgorod to the coast. There would be a serious unhappiness on many sides if somebody would try to interfere into this schema because weakening the trade would mean lesser profits for the Swedish and German merchants.

Now, as far as the evil Teutonic Order is involved, strictly speaking it was on a wrong side of Lithuania and the stories of its expansion to the East are grossly exaggerated. The entity involved were the leftovers of Livonian Brothers of the Sword that had been incorporated into the Teutonic Order and better known as Livonian Order (white on the map). It did not have numbers needed for any serious conquest and most of its time and energy had been spent upon the quarrels with Archbishop of Riga (to whom it was formally subordinated) and other local entities. The most advertised engagement, so-called Battle on Ice, in a reality was an ordinary border encounter led by the Bishop of Dorpat, whterritory was raided by the Novgorodian troops under Alexander. Some members of the Livonian Order did participate in it but there were no plans beyond repelling the looters. Not that a size of the armies involved (and a number of the knights) would allow any serious conquest. What was happening in a reality, was political game with Pskov. It was an independent principality until 1230 after which it became subordinated to Novgorod and was directly ruled from it until mid-XIII after which it started inviting its own princes again. Small wonder that in 1240 not everybody in Pskov was happy with the situation and that there was a party looking for the Livonian Order as an option. As a result, in the summer of 1240 Pskov accepted two Order’s brothers as city administrators. Which resulted in a retaliatory action from Novgorod: in 1242 Pskov was returned under the Novgorodian control and territory of the Bishopric of Derpt was invaded and looted. The Bishop raised whatever troops he could, defeated one of the looting bands and then was defeated himself. The mysterious invading “Germans” of the official imperial/Soviet history who presumably threatened Novgorod itself (*) never were fully identified.

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The Mongolian factor. The Novgorod Republic voluntarily submitted to the Mongols and paid tribute in 1241. From that point on invasion by the <whatever> Order and pretty much anybody else (with the possible exception of the ASBs and even this is not guaranteed) would mean the Mongolian involvement: attack on Khan’s vassal was an offense to the Khan. In the XIII century a number of the suicidal maniacs even among the military orders and clergy was too limited to launch a major war with the odds being that bad. Actually, at some later time there was an idea of attacking Novgorod which initially generated some enthusiasm but at the news that the GH is sending it’s troops to the area the “crusade” was speedily disbanded. 😂
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(*) Officially, it looked this way. The “Germans” (of unidentified origin and numbers) took castle of Koporie (see below) and advanced within 30 km from Novgorod. At which point Novgorod decided to call back Prince Alexander (who was expelled from Novgorod in previous year and was in Pereslavl-Zalessky, approximately 400 km away from Novgorod). Alexander sent to them his brother, Andrew, who was rejected and Alexander was asked for the second time after which he arrived with his troops. All that time the evil “invaders” did not move a step closer to Novgorod. Now, look at the size of Koporie and try to figure out how many troops it could hold. Now, if somebody still seriously believes in that scenario (actually, millions of people did thanks to the skillful propaganda), I have a very nice bridge for sale. 😂
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The powerful Swedish leader at the time was Birger, and Spiridon is not that far off phonetically.
But there is no documented trace of Birger participating in any attack on Novgorod in 1240 and, on a top of it, being wounded to the face during the expedition ( in which he did not participate). Personally, I can’t find too much of a phonetic similarity between these two names: it seems like the Sholem Aleichem’s explanation of how to make “Albert” out of “Chaim” 🤪
 
Swedish sources state that Birger Jarl was home to make his wife pregnant before the battle, and that the campaign most likely was a private venture by Bishop Thomas of Åbo, who was a very ambitious man trying to expand his own and catholic influence in the area - he was later caught faking papal letters and having tortured and exectured a man and had to resign and enter the Dominican order as a simple brother 1245.

Assuming this was a raid-plunder-crusade along the lines of earlier expeditions into Finland and Tavastlland, a victory would have resulted in looting and force-conversion, and then a return several years later to enforce actual tax payments and tithing. However, I doubt Sweden has the military power to actually enfore any kind of rule in Ingria in this era - the Ledung system was outdated and provided a mediocre force of medium infantry sailing on snäckor (which were soundly beaten by cogs in this era).

Barring some kind of calamity striking Novgorod (maybe an actual Mongol invasion), a second Swedish expedition would probably fare like the first did OTL (if it even happened, the sources are extremely limited).
 
Swedish sources state that Birger Jarl was home to make his wife pregnant before the battle, and that the campaign most likely was a private venture by Bishop Thomas of Åbo, who was a very ambitious man trying to expand his own and catholic influence in the area - he was later caught faking papal letters and having tortured and exectured a man and had to resign and enter the Dominican order as a simple brother 1245.

Assuming this was a raid-plunder-crusade along the lines of earlier expeditions into Finland and Tavastlland, a victory would have resulted in looting and force-conversion, and then a return several years later to enforce actual tax payments and tithing. However, I doubt Sweden has the military power to actually enfore any kind of rule in Ingria in this era - the Ledung system was outdated and provided a mediocre force of medium infantry sailing on snäckor (which were soundly beaten by cogs in this era).

Barring some kind of calamity striking Novgorod (maybe an actual Mongol invasion), a second Swedish expedition would probably fare like the first did OTL (if it even happened, the sources are extremely limited).
A Bishop is more likely because the earlier Russian source explicitly mentioning an unnamed bishop being present. However, there is no indication that the whole affair, if it did happen, was of any significance (and Alexander was expelled from Novgorod the next year) or that a force involved was of a size capable of threatening Novgorod and forcing it to pay a tribute. At best the raiders would be able to take/destroy some small town(s), which was quite common o; both sides. Even holding these places was problematic as had been demonstrated during the campaign which ended by the battle on Peipus.
 
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