Segment 4 - Morty
After dealing with the weird tree, we capture 2 Pidgeottos, 1 Ledian and 1 Ariados.
In the Burned Tower we capture Koffing, Weezing and Raticate, as well as unlock the Roaming Dogs.
After that a combination of Quilava and Croconaw beat Morty.
Pidgeotto, Raticate, Koffing, Weezing, Ledian, Ariados (+ 6)
72 / 1102 (6.5 %)
Chuck and Jasmine
A quick jaunt left and we get Tauros and Miltank on our way to Olivine. We also find Entei and Raikou so they're on our Pokedex for when we want to hunt them down later.
While going to Cianwood, Bayleef, Croconaw and Quilava evolve. I then collect a Shuckle in Cianwood.
Tauros, Meganium, Typhlosion, Feraligatr, Shuckle, Miltank (+ 6)
78 / 1102 (7.1 %)
Segment 6 - Pryce
Now that we have Surf, Strength and Fly we can backtrack and get a few more Pokémon we had to pass up.
On Route 30 we catch 3 Poliwhirls, then we drop by the Union Cave where we get Lapras and after a bit of wandering, we reach the Ruins of Alph and get Natu and Smeargle.
In Slowpoke Well we get Slowpoke, Slowbro and a King's Rock to evolve one of our Poliwhirls into Politoed.
On Route 42, we get Goldeen, Seaking, Fearow and Arbok. Then we go onwards to the Lake of Rage, passing by Route 43 where we nab Farfetch'd and Furret.
Drowzee evolved while in Rocket HQ. After some phone manip I manage to get a Water Stone and evolve the final Poliwhirl to Poliwrath and then I beat Pryce.
Fearow, Arbok, Poliwhirl, Poliwrath, Slowpoke, Slowbro, Farfetch'd, Hypno, Goldeen, Seaking, Lapras, Furret, Natu, Politoed, Smeargle (+ 15)
93 / 1102 (8.4 %)
Segment 7 - Clair
After that I went to Olivine and captured Chinchou which I had forgotten to do so previously, then did the Team Rocket Radio subplot. In the process, Pidgeotto evolved.
After that I took a quick detour to Ecruteak where I capture Suicune and boxed Feraligatr. On Route 44 we get two Weepinbells, and after some clock manip we can evolve one of them into Victreebell.
On the Ice Path we get a Jynx and after reaching Blackthorn, go back to Goldenrod and breed a Smoochum. On Route 45, we grab a Skarmory, and then we go beat Clair.
After proving ourselves in the Dragon Den we get a gift Dratini.
Pidgeot, Weepinbell, Victrebeel, Jynx, Dratini, Chinchou, Skarmory, Smoochum, Suicune (+ 9)
102 / 1102 (9,3 %)
Segment 8 - Elite 5 and Kanto
On Route 27, we capture Doduo and Dodrio and on Rt. 26 we get a Sandslash, and then we beat the Pokemon League.
As we traverse through Kanto we get 3 Gloom on Rt. 24, and then we go back to Johto to get 2 Seel and Lugia on the Whirl Islands as well as get some stones to let us evolve Gloom into Vileplume and Bellossom.
On the way to Fuchsia, one of the Seels evolved. Then we finish beating Gym Leaders and quickly get Venomoth, Granbull and 2 Slugmas around Kanto before returning to Johto for the last time.
Back in Johto, we go to Olivine to get Lanturn, then Blackthorn to get Dragonair, and drop by Azalea to start the GS event and ultimately get Celebi.
And now we get to the hard part: Getting Raikou and Entei. Once we get them, we can get Ho-Oh and end the game but until then we need them. Now, we can get one pretty much for free (as "free" as just finding one can be) with the Master Ball, but the other one's gonna be tricky.
After a while I used my Master Ball on Raikou and I legit lucked out with Entei, managed to get it with one Ultra Ball at full health. Thanks, Lady Luck.
After that, I eventually made my way to Ho-Oh and captured it, leaving me only one Pokemon to get: Magcargo. After some Victory Road training and a few Rare Candies, I got it and can end the game.
Sandslash, Gloom, Vileplume, Venomoth, Doduo, Dodrio, Seel, Dewdong, Dragonair, Lanturn, Bellossom, Granbull, Slugma, Magcargo, Raikou, Entei, Lugia, Ho-Oh, Celebi (+ 19)
121 / 1102 (11.0 %)
With that we're officially past the 10% mark! Here's the final box shot combined from PkHeX.
In the interest of transparency, I couldn't figure out how to make PkHeX recognize Celebi as legit, probably because I was playing in actual Crystal instead of VC Crystal, so that's why there's the red triangle there. Still, it's as legit as possible and it was caught in-game.