SW, thanks for posting.
No; you're definitely not alone. Fatigue--along with joint pain, general malaise, and sometimes, fever--are common complaints during flares, and even just before a flare. (Many folks with IBD know that they're about to flare specifically because they feel those "flu-ish" feelings coming on.)
And, yes; you are right. One reason for feeling the way you do, is your body's reaction to inflammation. It is thought that IBD is an autoimmune disease; so, in effect, your body is somehow, fighting itself.
If you are chronically anemic due to your disease, and/or you actively bleed during your flares, this may be another reason for your fatigue. Also, nutritional problems related to your IBD could be at play, as well.
Be well,
Hope