So I used to run a 6:20/mile pace 5k. Then, I started riding a bike and training for an IM. I went from never riding a bike to doing 6 hours in my IM in Choo. All my training on Trainerroad.

During that time, my running pace slowed into the high 8 to low 9 minute per mile pace

After Choo, I took time off the bike for about ,2 months (hurt my knee). During that time, my running pace came back. My swim pace also improved by 10 secs per 100 yards on straight 3500yd sets.

Then, I started bike training again. My run is getting slower, and my swim time is already back to where it was when I was cycling
Why is the bike making me Slower? I mainly do 3-4 1.5-2.5 hour sweet spot interval type rides at 85% ftp

I mainly do 3-4 1.5-2.5 hour sweet spot interval type rides at 85% ftp

I'm a relative novice, but it doesn't seem to be expected that your run pace/fitness would necessarily decrease because you are taking on swim and bike training. To me, it sounds like maybe an overtraining issue. If you're adding a relatively heavy load of bike training, your legs might just be too fatigued to perform as you expect on the run.

I started structured bike (and swim) training in the fall, and my run pace has only improved, in spite of reducing my run volume. I was never a high volume runner, but I used to average 2-3 runs per week for a total of ~15 miles. My typical 5k pace was in the 6:50-7:00/mi range. Since I started bike (2-3 times a week) and swim training (3-4 times a week) in October, I've reduced my runs down to 1-2 per week. I'm running faster than I ever have before. Sure, it's n=1, but I think in general if you're not overtraining and you have a decent base of run fitness, adding in bike and swim, should improve your run fitness.

You are incorrect about assuming that your run pace will necessarily improve by bike training.

If you are a novice runner, then sure, nearly anything you do added with your legs will help - cycling, jumping, skiing, basketball, etc. mainly because your level of performance and expectations are nowhere near your potential.

However, if you have a decent level of prior run training regular volume and speed, if you do not maintain that level of run training (because you are cycling a lot more), you will take a hit on your running compared to your prior performance. You can minimize the hit to running by doing a lot more biking to compensate, but at some point not too far along, you will have to run more to improve running rather than hoping for bike x-over.

The OPs description is exactly how I felt after following the Trainerroad Oly Build plan, which I've posted about on other threads, but I really feel is too hard for its own good. There are zero easy rides, and three hard rides per week - one VO2max crushingly hard workout, one hard steady state workout, and one long but surprisingly punishing long 90min ish SS workout. The run used to be my strength, but after the TR cycle, I was unable to run anywhere near my normal (modest) training amount due to the bike beatdown, and I lost more on the run than I gained on the bike on race day. (Not to mention swim losses...)

Consider yourself lucky if you can run 1 day per week, bike the other days, and pull off sprint/Oly runs in the sub7:00/mi range, unless you were a decently good runner beforehand.

^This is your answer.

Way too much intensity to fit in proper run and swim volume/intensity without accumulating fatigue and seeing overall performance losses rather than gain. Keeping overall volume intact, reduce to sweet spot work to 1 (2 max) one hour to 1.5 hours per week. The rest of your riding volume should be more in the ballpark of 70%, with some low to mid tempo (76-80%) mixed in and see what that does for you over a few weeks. Generally your running should be at "normal" speeds (not IM pace). If you're not hitting that regularly/within 10% of that AND not recovering day-to-day, then usually its a) too much intensity either running or cycling, and or b) poor functional threshold/pace estimates (which also leads to too much intensity).