Question: I'm an Indian passport holder. My brother and I are planning a 2-week trip through South East Asia namely Thailand, Singapore, and Malaysia (in that order). This week I'll be applying for visas through VFS global (not sure if there is any other way). Anyway, since India is the country where all these visas will be issued, I wonder the following:

Are we expected to enter Singapore and Malaysia from India? We want to enter Singapore from Thailand and Malaysia from Singapore (all by air and not road), are we allowed to do so?

Answer: 
A visa is permission to enter a country.

Where you're coming *from* doesn't matter. If you have a visa permitting you to entry country x, you can arrive in x from any other country. (There are restrictions on ports of entry for some travel between India and Nepal, and sometimes other country combinations, but that's not asked-about in this question.)

It's worth noting that in the current time of covid, there are often covid-specific requirements as well: while some countries in the recent past refused entry to travelers who've been in other, specified locations during the past days or weeks, those prohibitions have disappeared. Many countries do, however, require travelers to show proof of vaccination or to quarantine. A reputable source for such travel information is [Sherpa](https://apply.joinsherpa.com/map?affiliateId=sherpa&language=en-US). Both Singapore and Malaysia require quarantine if the traveler is unvaccinated.
Some specific answer for this itenary.

Yes, you are allowed to enter from any country, provided your visa rule allows that. I have travelled 7 countries successively once and there was no issues.

Regarding your itenary, you can take visa as follows.

1. Thailand has visa on arrival. You have to take travel insurance that covers covid. For Thai airways and most other, it might be included in airfare, or there is a box to check to purchase. See when you book that. No need for VFSglobal.
2. Singapore. You have to take visa from any travel agent. You have to submit your bank statements and proof that you are working (or equivalent). You will usually get it in a week or so. You may have to submit the passport. You will get a separate paper to print and show. Get vaccination certificate from here - <https://go.gov.sg/vcp-portal> , After uploading your 'Travel vaccination certificate' from cowin, which contains your passport and date of birth. 3 days prior to arrival in Singapore, fill arrival card online - <https://eservices.ica.gov.sg/sgarrivalcard/>. If you have a friend or relative who is a PR/citizen of singapore, ask them to apply visa on your behalf. You can skip travel agent and proof of income and all and you will get visa in matter of hours.
3. Malaysia. You can take from here - <https://malaysiavisa.imi.gov.my/evisa/evisa.jsp>. Although eNTRI is enough for your case, take eVisa to avoid any hassles. Pay fees online and you will get visa within a day or so. I am not sure about vaccination requirements and all.

Some tips.

1. You can travel to Malaysia from Singapore using land border. You can book from easybook.com. Take a bus that goes via Tuas link for faster clearance. Don't take during weekends, as it can take hours to cross the border. Its cheapest way.
2. Take a travel insurance that covers covid for the whole trip. If you get covid, especially in Singapore, hospitalization and isolation facilities will cost too much.
3. Always carry prescription for medications you are bringing.
4. Although RT-PCR is not required, it would be wise to test before journey and carry the results.

Happy journey.