In the top-of-the-table clash, Meghalaya resumed the day at 294 for five but Dhapola (6/52) was at his menacing best, bundling out their rivals for addition of just 17 runs.
This was Dhapola's fourth five-wicket haul in as many matches and the 28-year-old now has 32 wickets from four games.
In Dimapur, Nagaland offspinner Tahmeed Rahman claimed a hat-trick on way to a 5/108, but they found themselves on the mat, trailing by 60 runs with six wickets in hand in the second innings.
Rahman claimed Samson Singh, Kabrambam Meitei and Nungleppam Singh off consecutive deliveries in the 77th over to have Manipur at 273/8. But Raghav found able company in number ten batsman Thokchom Singh, added 62 runs and completed a double century.
Thokchom scored only eight runs before becoming Rahman's fifth victim.
In reply, Nagaland were 150/4 in their second innings with KB Pawan (47) and Arbar Kazi (24) seeing through the day.
In Patna, Indrajit Kumar (overnight on 127) smashed 222 while skipper Babul Kumar (overnight 72) missed out on a century by two runs as Bihar piled misery on Arunachal Pradesh to declare their first innings for 536/5.
Arunachal Pradesh, who were skittled out for 84 on day one, finished day two at 98/1, still trailing Bihar by 354 runs.
In Dehradun: Meghalaya 311; 95.5 overs (Puneet Bisht 154, Yogesh Nagar 91; Deepak Dhapola 6/52, Sunny Rana 2/73, Dhanraj Sharma 2/81). Uttarakhand 175/4; 73 overs (Vineet Saxena 62 batting, Rajat Bhatia 54 batting; Dipu Sangma 2/26).
In Dimapur: Nagaland 126 and 150/4; 42 overs (Rongsen Jonathan 59, KB Pawan 47 batting; Bishworjit Konthoujam 2/29, Kabrambam Meitei 2/35). Manipur 336; 91.4 overs (Mayank Raghav 228; Tahmeed Rahman 5/108, Pawan Suyal 2/76).
In Patna: Arunachal Pradesh 84 and 98/1; 26 overs (Samarth Seth 52 batting). Bihar 536/5 declared; 112 overs (Indrajit Kumar 222, Babul Kumar 98, Utkarsh Bhaskar 57, K Rajnish 45, MD Rahmatullah 42; Myendung Singpho 2/90).
In Wayanad: Puducherry 647/8 declared; 157 overs (Paras Dogra 253, Fabid Ahmed 99, Saju Chothan 81, Vikneshwaran Marimuthu 78, Damodaren Rohit 59; Ishwar Chaudhary 2/118, Bipul Sharma 2/141, Lee Yong Lepcha 2/173).
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